U.S. patent number 7,345,142 [Application Number 11/043,824] was granted by the patent office on 2008-03-18 for nucleotide and amino acid sequences, and assays and methods of use thereof for diagnosis of cardiac disease.
This patent grant is currently assigned to Compugen Ltd.. Invention is credited to Michal Ayalon-Soffer, Yossi Cohen, Gad S. Cojocaru, Dvir Dahary, Alexander Diber, Guy Kol, Zurit Levine, Amit Novik, Sarah Pollock, Shirley Sameah-Greenwald, Osnat Sella-Tavor, Ronen Shemesh, Amir Toporik, Shira Walach.
United States Patent |
7,345,142 |
Cohen , et al. |
March 18, 2008 |
Nucleotide and amino acid sequences, and assays and methods of use
thereof for diagnosis of cardiac disease
Abstract
Novel markers for cardiac disease that are both sensitive and
accurate. These markers are differentially and/or specifically
expressed in cardiac tissue, as opposed to other types of tissues,
optionally and preferably including muscle tissue. The measurement
of these markers, alone or in combination, in patient samples
provides information that the diagnostician can correlate with a
probable diagnosis of cardiac disease, including pathology and/or
damage, including acute and/or chronic damage. The markers of the
present invention, alone or in combination, show a high degree of
differential detection between cardiac disease states and
non-cardiac disease states.
Inventors: |
Cohen; Yossi (Banstead,
GB), Diber; Alexander (Rishon-LeZion, IL),
Toporik; Amir (Azur, IL), Pollock; Sarah
(Tel-Aviv, IL), Levine; Zurit (Herzlia,
IL), Ayalon-Soffer; Michal (Ramat-HaSharon,
IL), Cojocaru; Gad S. (Ramat-HaSharon, IL),
Novik; Amit (Beit-HaSharon, IL), Kol; Guy (Givat
Shmuel, IL), Sella-Tavor; Osnat (Kfar Kish,
IL), Walach; Shira (Hod-HaSharon, IL),
Sameah-Greenwald; Shirley (Kfar-Saba, IL), Dahary;
Dvir (Tel-Aviv, IL), Shemesh; Ronen (Modiln,
IL) |
Assignee: |
Compugen Ltd. (Tel Aviv,
IL)
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Family
ID: |
36757020 |
Appl.
No.: |
11/043,824 |
Filed: |
January 27, 2005 |
Prior Publication Data
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Document
Identifier |
Publication Date |
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US 20060172311 A1 |
Aug 3, 2006 |
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Related U.S. Patent Documents
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Filing Date |
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Issue Date |
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60620916 |
Oct 22, 2004 |
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60628123 |
Nov 17, 2004 |
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60621131 |
Oct 25, 2004 |
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60628134 |
Nov 17, 2004 |
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60622320 |
Oct 27, 2004 |
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60628190 |
Nov 17, 2004 |
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60630559 |
Nov 26, 2004 |
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60539129 |
Jan 27, 2004 |
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60539128 |
Jan 27, 2004 |
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Current U.S.
Class: |
530/300 |
Current CPC
Class: |
C07K
14/705 (20130101); C12Q 1/6883 (20130101); G01N
33/6893 (20130101); G01N 2800/324 (20130101); G01N
2800/325 (20130101); G01N 2800/327 (20130101); C12Q
2600/156 (20130101); C12Q 2600/158 (20130101) |
Current International
Class: |
A61K
38/00 (20060101) |
Foreign Patent Documents
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4243648 |
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Jul 1994 |
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DE |
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WO 00/23585 |
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Apr 2000 |
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WO |
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WO 01/32927 |
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May 2001 |
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WO |
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Other References
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examiner .
Sequence comparison. cited by examiner .
PCT Written Opinion Of The International Searching Authority for
PCT/IB2005/001306 (In English). cited by other .
Isolation and Characterization of the Human Cardiac Troponin I Gene
(TNNI3), Bhavsar et al., Article No. 0317, Genomics 35., pp. 11-23
(1996) (In English). cited by other .
Thin-filament-binding domains of cardiac and fast skeletal muscle
troponin I isoforms as studied by epitope tagging, Toyota et al.,
Journal of Muscle Research and Cell Motility, 20:755-760, 1999 (in
English). cited by other .
Alu-Containing Exons are Alternatively Spliced, Sorek et al.,
Department of Zoology, pp. 1060-1067 (in English). cited by other
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XP-002366938 BQ230791 standard, National Institutes of Health,
Mammalian Gene Collection, Contact: Dr. Robert Strausberg (1 pg.)
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PCT Preliminary Report on Patentability dated Aug. 3, 2006 for PCT
Application No. PCT/IB2005/001306, In English. cited by
other.
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Primary Examiner: Yu; Misook
Assistant Examiner: Aeder; Sean E
Attorney, Agent or Firm: Staas & Halsey LLP
Parent Case Text
CROSS-REFERENCE TO RELATED APPLICATION(S)
This application is related to Novel Nucleotide and Amino Acid
Sequences, and Assays and Methods of use thereof for Diagnosis of
Cardiac Disease, and claims priority to the below U.S. provisional
applications which are incorporated by reference herein:
Application No. 60/620,916 filed Oct. 22, 2004--Differential
Expression of Markers in Colon Cancer Application No. 60/628,123
filed Nov. 17, 2004--Differential Expression of Markers in Colon
Cancer II Application No. 60/621,131 filed Oct. 25,
2004--Diagnostic Markers for Colon Cancer, and Assays and Methods
of use thereof. Application No. 60/628,134 filed Nov. 17,
2004--Differential Expression of Markers in Ovarian Cancer II
Application No. 60/622,320 filed Oct. 27, 2004--Diagnostic Markers
for Cardiac Disease and/or Pathological Conditions, and Assays and
methods of Use thereof. Application No. 60/628,190 filed Nov. 17,
2004--Diagnostic Markers for Cardiac Disease and/or Pathological
Conditions, and Assays and Methods of Use thereof II Application
No. 60/630,559 filed Nov. 26, 2004--Diagnostic Markers for Cardiac
Disease and/or Pathological Conditions, and Assays and Methods of
Use thereof II Application No. 60/539,129 filed Jan. 27,
2004--Methods and Systems for Annotating Biomolecular Sequences
Application No. 60/539,128 filed Jan. 27, 2004--Evolutionary
Conserved Spliced Sequences and Methods and Systems for Identifying
thereof
Claims
What is claimed is:
1. An isolated polypeptide comprising the protein set forth in SEQ
ID NO: 303.
2. An isolated polypeptide comprising a the polypeptide having set
forth in SEQ ID NO. 413.
3. A biomarker for detecting heart disorders, comprising the
Drotein set forth in SEQ ID NO. 413 marked with a label.
4. A composition consisting essentially of the polypeptide set
forth in SEQ ID NO. 413.
5. A composition consisting essentially of the polypeptide set
forth in SEQ ID NO. 303.
6. A biomarker for detecting heart disorders consisting essentially
of the protein set forth in SEQ ID NO. 303 marked with a label.
7. The biomarker of claim 3, wherein the label is selected from the
group consisting of magnetic beads, fluorescent dyes, radiolabels,
horse radish peroxide, alkaline phosphatase, colloidal gold,
colored glass beads and plastic beads.
8. The biomarker of claim 6, wherein the label is selected from the
group consisting of magnetic beads, fluorescent dyes, radiolabels,
horse radish peroxide, alkaline phosphatase, colloidal gold,
colored glass beads and plastic beads.
Description
FIELD OF THE INVENTION
The present invention is related to novel nucleotide and protein
sequences that are diagnostic markers for cardiac disease and/or
pathological conditions, including cardiac damage, and assays and
methods of use thereof.
BACKGROUND OF THE INVENTION
Cardiovascular diseases are an important cause of mortality and
morbidity. Amongst all age groups considered, IHD is the most
common cause of death not only in men but also in women. Coronary
atherosclerosis is a chronic progressing process, associated with
angina type symptoms and frequently result in Acute Myocardial
Infarction (AMI). The diagnosis is achieved with a combination of
patient physical examination, ECG since 1950's molecular markers
play the most important role in the differential diagnosis of AMI
from other conditions with similar symptoms. Early diagnosis is
mandatory of the establishment of early treatment (including blood
diluting agents, thrombolysis, catheterization and surgery).
Early molecular markers for AMI were SGOT and LDH were proved to be
of very low specificity and are hardly being used at present. These
markers were replaced by CPK, and later on by the heart specific
CPK-MB variant. Its specificity is better than for SGOT and LDH, it
is still limited both in specificity and sensitivity which reach
only 67% when used together with electrocardiogram. In addition,
cardiac surgery, myocarditis, and electrical cardioversion often
result in elevated serum levels of the CPK-MB isoenzyme. Small
infarct with minor myocardial cell necrosis often do not increase
serum CPK-MB to a detected level. Myoglobin is another heart damage
low molecular (17 kD) protein but is even less specific to heart
muscle compared with CPK-MB. Its advantage over CPK-MB is a rapid
rise from the onset of symptoms--usually between 3-6 hours. It is
considered one of the earliest indicators (together with H-FABP)
but it lacks specificity due to significant expression in skeletal
muscle--its concentration is approximately two-fold lower in
cardiac than skeletal muscle and the leads to seriously diminished
specificity.
Cardiac troponins are currently the routine serum cardiac markers
used for the diagnosis of AMI. Troponin-I and Troponin-T have amino
acid sequences different from those of the skeletal muscle called
cTnT and cTnI (cardiac Troponin-T and I recpectively). Cardiac
troponins are not found in the serum of healthy individuals and
rise to up to 20 times above a predefined cut-off level, therefore
are very useful and sensitive in the detection of cardiac damage.
They are capable of detecting very small cardiac
damage--micro-infarction, it is associated with a very adverse
longer term prognosis. Cardiac troponin's sensitivity is
considerably higher than CPK-MB but they suffer from a few
disadvantages: 1. They are not early markers--cTnI and cTnT reach
peak serum value in about 12 and 48 hours respectively after
symptoms onset. 2. Levels of cTnI and cTnT remain elevated for up
to 10 days and 14 days respectively after AMI, therefore cannot be
used for the detection of re-infarction. 3. Other heart diseases
such as Congestive Heart Failure and Myocarditis can increase
troponins concentrations in the serum. The lack of specificity for
AMI is an advantage when there are other supporting clinical
evidence directing the doctor towards another diagnosis. Troponins
might have a diagnostic value in assessing myocardial damage after
coronary artery perfusion, monitoring progression and prognosis of
unstable angina, in the detection and prognosis of cardiac
contusion after blunt trauma, detecting myocarditis.
The heart specific variant H-FABP (Heart Fatty Acid binding
protein) is a low molecular protein (15 Kd) soluble non-enzyme
protein. H-FABP concentration in the heart muscle is greater than
that in skeletal muscle, and its normal baseline concentration is
several fold lower than myoglobin. In addition, it reaches peak
value in the urine and blood early, within 2-3 hours from AMI.
Within a period of 30-210 minutes after symptoms started, H-FABP
has higher sensitivity--up to 80%--when compared with other cardiac
markers (CPK-MB and the troponins sensitivity were reported to be
64% in the first 6 hours after AMI). Yet, H-FABP still misses every
5.sup.th patient in this time scale. H-FABP has other limitations
as well, including 1. rising in the plasma after exercise 2.
released from muscle in skeletal damage during the course of AMI
(like from intramuscular injections) 3. reduced clearance in renal
failure situations.
The search for novel cardiac damage markers is ongoing. Other
proteins are under trials for that purpose including glycogen
phosphorylase BB, HIF and VEGF 21.
SUMMARY OF THE INVENTION
Markers for the cardiac disease and/or cardiac pathology, including
but not limited to cardiac damage in the prior art are not
sufficiently sensitive and/or accurate, alone or in
combination.
The present invention overcomes these deficiencies of the
background art by providing novel markers for cardiac disease
and/or cardiac pathology, including but not limited to cardiac
damage that are both sensitive and accurate. Optionally and
preferably, these markers are detected in a biological sample.
According to preferred embodiments of the present invention,
cardiac disease and/or pathology and/or condition and/or disorder
may comprise one or more of Myocardial infarct, acute coronary
syndrome, angina pectoris (stable and unstable), cardiomyopathy,
myocarditis, congestive heart failure or any type of heart failure,
the detection of reinfarction, the detection of success of
thrombolytic therapy after Myocardial infarct, Myocardial infarct
after surgery, assessing the size of infarct in Myocardial infarct,
the differential diagnosis of heart related conditions from lung
related conditions (as pulmonary embolism), the differential
diagnosis of Dyspnea, and cardiac valves related conditions.
According to preferred embodiments of the present invention,
examples of suitable biological samples include but are not limited
to blood, serum, plasma, blood cells, urine, sputum, saliva, stool,
spinal fluid, lymph fluid, the external secretions of the skin,
respiratory, intestinal, and genitourinary tracts, tears, milk,
neuronal tissue, and any human organ or tissue. In a preferred
embodiment, the biological sample comprises cardiac tissue and/or a
serum sample and/or a urine sample and/or any other tissue or
liquid sample. The sample can optionally be diluted with a suitable
eluant before contacting the sample to the antibody.
Information given in the text with regard to cellular localization
was determined according to four different software programs: (i)
tmhmm (from Center for Biological Sequence Analysis, Technical
University of Denmark DTU, dot cbs dtu dot dk/services/TMHMM/TMHMM2
dot 0b dot guide dot php) or (ii) tmpred (from EMBnet, maintained
by the ISREC Bionformatics group and the LICR Information
Technology Office, Ludwig Institute for Cancer Research, Swiss
Institute of Bioinformatics, dot ch dot embnet dot
org/software/TMPRED_form dot html) for transmembrane region
prediction; (iii) signalp_hmm or (iv) signalp_nn (both from Center
for Biological Sequence Analysis, Technical University of Denmark
DTU, dot cbs dot dtu dot dk/services/SignalP/background/prediction
dot php) for signal peptide prediction. The terms "signalp_hmm" and
"signalp_.mu.nn" refer to two modes of operation for the program
SignalP: hmm refers to Hidden Markov Model, while nn refers to
neural networks. Localization was also determined through manual
inspection of known protein localization and/or gene structure, and
the use of heuristics by the individual inventor. In some cases for
the manual inspection of cellular localization prediction inventors
used the ProLoc computational plafform [Einat Hazkani-Covo, Erez
Levanon, Galit Rotman, Dan Graur and Amit Novik; (2004) "Evolution
of multicellularity in metazoa: comparative analysis of the
subcellular localization of proteins in Saccharomyces, Drosophila
and Caenorhabditis." Cell Biology International 2004;
28(3):171-8.], which predicts protein localization based on various
parameters including, protein domains (e.g., prediction of
trans-membranous regions and localization thereof within the
protein), pl, protein length, amino acid composition, homology to
pre-annotated proteins, recognition of sequence patterns which
direct the protein to a certain organelle (such as, nuclear
localization signal, NLS, mitochondria localization signal), signal
peptide and anchor modeling and using unique domains from Pfam that
are specific to a single compartment.
Information is given in the text with regard to SNPs (single
nucleotide polymorphisms). A description of the abbreviations is as
follows. "T->C", for example, means that the SNP results in a
change at the position given in the table from T to C. Similarly,
"M->Q", for example, means that the SNP has caused a change in
the corresponding amino acid sequence, from methionine (M) to
glutamine (Q). If, in place of a letter at the right hand side for
the nucleotide sequence SNP, there is a space, it indicates that a
frameshift has occurred. A frameshift may also be indicated with a
hyphen (-). A stop codon is indicated with an asterisk at the right
hand side (*). As part of the description of an SNP, a comment may
be found in parentheses after the above description of the SNP
itself. This comment may include an FTId, which is an identifier to
a SwissProt entry that was created with the indicated SNP. An FTId
is a unique and stable feature identifier, which allows
construction of links directly from position-specific annotation in
the feature table to specialized protein-related databases. The
FTId is always the last component of a feature in the description
field, as follows: FTId=XXX_number, in which XXX is the 3-letter
code for the specific feature key, separated by an underscore from
a 6-digit number. In the table of the amino acid mutations of the
wild type proteins of the selected splice variants of the
invention, the header of the first column is "SNP position(s) on
amino acid sequence", representing a position of a known mutation
on amino acid sequence.
SNPs may optionally be used as diagnostic markers according to the
present invention, alone or in combination with one or more other
SNPs and/or any other diagnostic marker. Preferred embodiments of
the present invention comprise such SNPs, including but not limited
to novel SNPs on the known (WT or wild type) protein sequences
given below, as well as novel nucleic acid and/or amino acid
sequences formed through such SNPs, and/or any SNP on a variant
amino acid and/or nucleic acid sequence described herein.
Information given in the text with regard to the Homology to the
known proteins was determined by Smith-Waterman version 5.1.2 using
special (non default) parameters as follows: model=sw.model
GAPEXT=0 GAPOP=100.0 MATRIX=blosum100
Information is given with regard to overexpression of a cluster in
cancer based on microarrays. As a microarray reference, in the
specific segment paragraphs, the unabbreviated tissue name was used
as the reference to the type of chip for which expression was
measured. There are two types of microarray results: those from
microarrays prepared according to a design by the present
inventors, for which the microarray fabrication procedure is
described in detail in Materials and Experimental Procedures
section herein; and those results from microarrays using Affymetrix
technology. As a microarray reference, in the specific segment
paragraphs, the unabbreviated tissue name was used as the reference
to the type of chip for which expression was measured. For
microarrays prepared according to a design by the present
inventors, the probe name begins with the name of the cluster
(gene), followed by an identifying number. Oligonucleotide
microarray results taken from Affymetrix data were from chips
available from Affymetrix lnc, Santa Clara, Calif., USA (see for
example data regarding the Human Genome U133 (HG-U133) Set at dot
affymetrix dot com/products/arrays/specific/hgu133 dot affx;
GeneChip Human Genome U133A 2.0 Array at dot affymetrix dot
com/products/arrays/specific/hgu133av2 dot affx; and Human Genome
U133 Plus 2.0 Array at dot affymetrix dot
com/products/arrays/specific/hgu133plus dot affx). The probe names
follow the Affymetrix naming convention. The data is available from
NCBI Gene Expression Omnibus (see dot ncbi dot nlm dot nih dot
gov/projects/geo/and Edgar et al, Nucleic Acids Research, 2002,
Vol. 30, No. 1 207-210). The dataset (including results) is
available from dot ncbi dot nlm dot nih dot gov/geo/query/acc dot
cgi?acc=GSE1133 for the Series GSE1133 database (published on March
2004); a reference to these results is as follows: Su et al (Proc
Natl Acad Sci USA. 2004 Apr. 20; 101(16):6062-7. Epub 2004 Apr.
09).
Oligonucleotide probes for use with arrays designed by the present
inventors:
TABLE-US-00001 >S67314_0_0_741 (SEQ ID NO 392)
CACAGAGCCAGGATGTTCTTCTGACCTCAGTATCTACTCCAGCTCCAGCT
>S67314_0_0_744 (SEQ ID NO 393)
TGGCATGCTGGAACATGGACTCTAGCTAGCAAGAAGGGCTCAAGGAGGTG
In the heart specific clusters, a first set of abbreviations is
used for the first histogram ADP=adipocyte BLD=blood BLDR=bladder
BRN=brain BONE=bone BM=bone marrow BRS=mammary gland CAR=cartilage
CNS=central nervous system COL=colon E-ADR=endocrine_adrenal_gland
E-PAN=endocrine_pancreas E-PT=endocrine_parathyroid_thyroid
ENDO=endocrine_unchar EPID=epididymis GI=gastrointestinal tract
GU=genitourinary HN=head and neck HRT=heart KD=kidney LI=liver
LUNG=lung LN=lymph node MUS=muscle OV=ovary PNS=peripheral nervous
system PRO=prostate SKIN=skin SPL=spleen SYN=synovial membrane
TCELL=immune T cells THYM=thymus TST=testes UTER=cervix-uterus
VAS=vascular
In the second histogram(s) of the heart paragraph, the oligo-probe
names are abbreviated/enumerated as follows:
TABLE-US-00002 "adipocyte", "A1"; "adrenalcortex", "A2";
"adrenalgland", "A3"; "amygdala", "A4"; "appendix", "A5";
"atrioventricularnode", "A6"; "bm_cd105_endothelial", "E1";
"bm_cd33_myeloid", "M1"; "bm_cd34_", "B1";
"bm_cd71_earlyerythroid", "E1"; "bonemarrow", "B2";
"bronchialepithelialcells", "B3"; "cardiacmyocytes", "C1";
"caudatenucleus", "C2"; "cerebellum", "C3"; "cerebellumpeduncles",
"C4"; "ciliaryganglion", "C5"; "cingulatecortex", "C6";
"globuspallidus", "G1"; "heart", "H1"; "hypothalamus", "H2";
"kidney", "K1"; "liver", "L1"; "lung", "L2"; "lymphnode", "L3";
"medullaoblongata", "M1"; "occipitallobe", "O1"; "olfactorybulb",
"O2"; "ovary", "O3"; "pancreas", "P1"; "pancreaticislets", "P2";
"parietallobe", "P3"; "pb_bdca4_dentritic_cells", "P4";
"pb_cd14_monocytes", "P5"; "pb_cd19_bcells", "P6"; "pb_cd4_tcells",
"P7"; "pb_cd56_nkcells", "P8"; "pb_cd8_tcells", "P9"; "pituitary",
"Pa"; "placenta", "Pb"; "pons", "Pc"; "prefrontalcortex", "Pd";
"prostate", "Pe"; "salivarygland", "S1"; "skeletalmuscle", "S2";
"skin", "S3"; "smoothmuscle", "S4"; "spinalcord", "S5";
"subthalamicnucleus", "S6"; "superiorcervicalganglion", "S7";
"temporallobe", "T1"; "testis", "T2"; "testisgermcell", "T3";
"testisinterstitial", "T4"; "testisleydigcell", "T5";
"testisseminiferoustubule", "S6"; "thalamus", "T7"; "thymus", "T8";
"thyroid", "T9"; "tonsil", "Ta"; "trachea", "Tb";
"trigeminalganglion", "Tc"; "uterus", "U1"; "uteruscorpus", "U2";
"wholeblood", "W1"; "wholebrain", "W2";
It should be noted that the terms "segment", "seg" and "node" are
used interchangeably in reference to nucleic acid sequences of the
present invention; they refer to portions of nucleic acid sequences
that were shown to have one or more properties as described below.
They are also the building blocks that were used to construct
complete nucleic acid sequences as described in greater detail
below. Optionally and preferably, they are examples of
oligonucleotides which are embodiments of the present invention,
for example as amplicons, hybridization units and/or from which
primers and/or complementary oligonucleotides may optionally be
derived, and/or for any other use.
As used herein the phrase "cardiac disease" includes any type of
cardiac pathology and/or disorder and/or damage, including both
chronic and acute damage, as well as progression from acute to
chronic damage of the heart, and also propagation of one acute
event to another acute event. An example of the latter may occur
when an infarct is followed by another infarct in a relatively
short period of time, such as within 24 hours for example. An
infarct may also lead to acute heart failure immediately after the
infarct, as another example. These non-limiting examples are
intended to demonstrate that cardiac disease may also comprise a
plurality of acute events.
The term "marker" in the context of the present invention refers to
a nucleic acid fragment, a peptide, or a polypeptide, which is
differentially present in a sample taken from patients having a
cardiac disease, such as acute cardiac damage for example, as
compared to a comparable sample taken from subjects who do not have
cardiac disease.
As used herein the phrase "differentially present" refers to
differences in the quantity of a marker present in a sample taken
from patients having cardiac disease as compared to a comparable
sample taken from patients who do not have cardiac disease. For
example, a nucleic acid fragment may optionally be differentially
present between the two samples if the amount of the nucleic acid
fragment in one sample is significantly different from the amount
of the nucleic acid fragment in the other sample, for example as
measured by hybridization and/or NAT-based assays. A polypeptide is
differentially present between the two samples if the amount of the
polypeptide in one sample is significantly different from the
amount of the polypeptide in the other sample. It should be noted
that if the marker is detectable in one sample and not detectable
in the other, then such a marker can be considered to be
differentially present. For example, in the case of acute cardiac
damage, it is possible that a marker (such as a protein or fragment
thereof) could optionally be present in a blood sample from the
patient, indicating the presence of damage; lack of presence of
such a marker (and/or presence at a low level) would therefore
optionally and preferably indicate a lack of such damage.
Alternatively, chronically damaged heart might cause a low level of
the marker to be present in the blood sample, while acute damage
would cause a high level to be present. One of ordinary skill in
the art could easily determine such relative levels of the markers;
further guidance is provided in the description of each individual
marker below.
As used herein the phrase "diagnostic" means identifying the
presence or nature of a pathologic condition. Diagnostic methods
differ in their sensitivity and specificity. The "sensitivity" of a
diagnostic assay is the percentage of diseased individuals who test
positive (percent of "true positives"). Diseased individuals not
detected by the assay are "false negatives." Subjects who are not
diseased and who test negative in the assay are termed "true
negatives." The "specificity" of a diagnostic assay is 1 minus the
false positive rate, where the "false positive" rate is defined as
the proportion of those without the disease who test positive.
While a particular diagnostic method may not provide a definitive
diagnosis of a condition, it suffices if the method provides a
positive indication that aids in diagnosis.
As used herein the phrase "diagnosing" refers to classifying a
disease or a symptom, determining a severity of the disease,
monitoring disease progression, forecasting an outcome of a disease
and/or prospects of recovery. The term "detecting" may also
optionally encompass any of the above.
Diagnosis of a disease according to the present invention can be
effected by determining a level of a polynucleotide or a
polypeptide of the present invention in a biological sample
obtained from the subject, wherein the level determined can be
correlated with predisposition to, or presence or absence of the
disease. It should be noted that a "biological sample obtained from
the subject" may also optionally comprise a sample that has not
been physically removed from the subject, as described in greater
detail below.
As used herein, the term "level" refers to expression levels of RNA
and/or protein or to DNA copy number of a marker of the present
invention.
Typically the level of the marker in a biological sample obtained
from the subject is different (i.e., increased or decreased) from
the level of the same variant in a similar sample obtained from a
healthy individual (examples of biological samples are described
herein).
Numerous well known tissue or fluid collection methods can be
utilized to collect the biological sample from the subject in order
to determine the level of DNA, RNA and/or polypeptide of the
variant of interest in the subject.
Examples include, but are not limited to, fine needle biopsy,
needle biopsy, core needle biopsy and surgical biopsy (e.g., brain
biopsy), and lavage. Regardless of the procedure employed, once a
biopsy/sample is obtained the level of the variant can be
determined and a diagnosis can thus be made.
Determining the level of the same variant in normal tissues of the
same origin is preferably effected along-side to detect an elevated
expression and/or amplification and/or a decreased expression, of
the variant as opposed to the normal tissues.
A "test amount" of a marker refers to an amount of a marker present
in a sample being tested. A test amount can be either in absolute
amount (e.g., microgram/ml) or a relative amount (e.g., relative
intensity of signals).
A "test amount" of a marker refers to an amount of a marker in a
subject's sample that is consistent with a diagnosis of cardiac
disease. A test amount can be either in absolute amount (e.g.,
microgram/ml) or a relative amount (e.g., relative intensity of
signals).
A "control amount" of a marker can be any amount or a range of
amounts to be compared against a test amount of a marker. For
example, a control amount of a marker can be the amount of a marker
in a patient with cardiac disease or a person without cardiac
disease. A control amount can be either in absolute amount (e.g.,
microgram/ml) or a relative amount (e.g., relative intensity of
signals).
"Detect" refers to identifying the presence, absence or amount of
the object to be detected.
A "label" includes any moiety or item detectable by spectroscopic,
photo chemical, biochemical, immunochemical, or chemical means. For
example, useful labels include .sup.32P, .sup.35S, fluorescent
dyes, electron-dense reagents, enzymes (e.g., as commonly used in
an ELISA), biotin-streptavadin, dioxigenin, haptens and proteins
for which antisera or monoclonal antibodies are available, or
nucleic acid molecules with a sequence complementary to a target.
The label often generates a measurable signal, such as a
radioactive, chromogenic, or fluorescent signal, that can be used
to quantify the amount of bound label in a sample. The label can be
incorporated in or attached to a primer or probe either covalently,
or through ionic, van der Waals or hydrogen bonds, e.g.,
incorporation of radioactive nucleotides, or biotinylated
nucleotides that are recognized by streptavadin. The label may be
directly or indirectly detectable. Indirect detection can involve
the binding of a second label to the first label, directly or
indirectly. For example, the label can be the ligand of a binding
partner, such as biotin, which is a binding partner for
streptavadin, or a nucleotide sequence, which is the binding
partner for a complementary sequence, to which it can specifically
hybridize. The binding partner may itself be directly detectable,
for example, an antibody may be itself labeled with a fluorescent
molecule. The binding partner also may be indirectly detectable,
for example, a nucleic acid having a complementary nucleotide
sequence can be a part of a branched DNA molecule that is in turn
detectable through hybridization with other labeled nucleic acid
molecules (see, e.g., P. D. Fahrlander and A. Klausner,
Bio/Technology 6:1165 (1988)). Quantitation of the signal is
achieved by, e.g., scintillation counting, densitometry, or flow
cytometry.
Exemplary detectable labels, optionally and preferably for use with
immunoassays, include but are not limited to magnetic beads,
fluorescent dyes, radiolabels, enzymes (e.g., horse radish
peroxide, alkaline phosphatase and others commonly used in an
ELISA), and calorimetric labels such as colloidal gold or colored
glass or plastic beads. Alternatively, the marker in the sample can
be detected using an indirect assay, wherein, for example, a
second, labeled antibody is used to detect bound marker-specific
antibody, and/or in a competition or inhibition assay wherein, for
example, a monoclonal antibody which binds to a distinct epitope of
the marker are incubated simultaneously with the mixture.
"Immunoassay" is an assay that uses an antibody to specifically
bind an antigen. The immunoassay is characterized by the use of
specific binding properties of a particular antibody to isolate,
target, and/or quantify the antigen.
The phrase "specifically (or selectively) binds" to an antibody or
"specifically (or selectively) immunoreactive with," when referring
to a protein or peptide (or other epitope), refers to a binding
reaction that is determinative of the presence of the protein in a
heterogeneous population of proteins and other biologics. Thus,
under designated immunoassay conditions, the specified antibodies
bind to a particular protein at least two times greater than the
background (non-specific signal) and do not substantially bind in a
significant amount to other proteins present in the sample.
Specific binding to an antibody under such conditions may require
an antibody that is selected for its specificity for a particular
protein. For example, polyclonal antibodies raised to seminal basic
protein from specific species such as rat, mouse, or human can be
selected to obtain only those poyclonal antibodies that are
specifically immunoreactive with seminal basic protein and not with
other proteins, except for polymorphic variants and alleles of
seminal basic protein. This selection may be achieved by
subtracting out antibodies that cross-react with seminal basic
protein molecules from other species. A variety of immunoassay
formats may be used to select antibodies specifically
immunoreactive with a particular protein. For example, solid-phase
ELISA immunoassays are routinely used to select antibodies
specifically immunoreactive with a protein (see, e.g., Harlow &
Lane, Antibodies, A Laboratory Manual (1988), for a description of
immunoassay formats and conditions that can be used to determine
specific immunoreactivity). Typically a specific or selective
reaction will be at least twice background signal or noise and more
typically more than 10 to 100 times background.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
selected from the group consisting of SEQ ID NOs: 1, 2, 3 and
4.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
selected from the group consisting of SEQ ID NOs: 65, 66, 67, 68,
69, 70, 71 and 72.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
selected from the group consisting of SEQ ID NOs: 281, 282, 283 and
284.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
selected from the group consisting of SEQ ID NOs: 5, 6, 7, 8, 9 and
10
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
selected from the group consisting of SEQ ID NOs: 73, 74, 75, 76,
77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93
and 94.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
selected from the group consisting of SEQ ID NOs: 285, 286, 287,
288, 289, 290 and 291
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 12, 13, 14, 15,
16 and 17
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 95, 96, 97, 98,
99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
112.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 292, 293, 294,
295 and 296
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 18 and 19.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 113, 114, 115,
116, 117, 118, 119, 120, 121 and 122.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 297 and 298.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 20 and 21.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 123, 124, 125,
126, 127, 128 and 129.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 299 and 300.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 26, 27, 28, 29
and 30.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 150, 151, 152,
153, 154, 155, 156, 157, 158, 159, 160, 161, 162 and 163.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 305; 306; 307 and
308
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 31, 32, 33, 34,
35, 36 and 37.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 164, 165, 166,
167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179,
180, 181, 182, 183, 184, 185 and 186
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 309, 310, 311 and
312.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 38, 39, 40 and
41.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 187, 188, 189,
190, 191, 192, 193, 194, 195 and 196.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 313, 314, 315 and
316.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 42, 43, 44, 45,
46, 47, 48, 49 and 50.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 197, 198, 199,
200, 201, 202, 203, 204, 205, 206, 207 and 208.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 317, 318, 319,
320, 321, 322, 323, 324 and 325.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs:51, 52, 53, 54,
55, 56, 57, 58, 59 and 60.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
SELECTED FROM THE GROUP CONSISTING OF SEQ ID NOs: 209 to 273.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
selected from the group consisting of SEQ ID NOs: 326 to 334.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a transcript
selected from the group consisting of SEQ ID NOs: 22-25, 353 or
386.
According to preferred embodiments of the present invention, there
is provided an isolated polynucleotide comprising a segment
selected from the group consisting of SEQ ID NOs: 130-149.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide comprising a protein variant
selected from the group consisting of SEQ ID NOs: 301-304, 325,
354-356 or 387.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 326, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-1855 of SEQ ID NO.338, which also
corresponds to amino acids 1-1855 of SEQ ID NO.326, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 1856-1904 of SEQ ID NO. 326, wherein
said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 326, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VRRTPDTGSRCGSFFSGPTAPPSQGSSHLLLEMLLVDLTFFSRSAVSLT
(SEQ ID NO:394) in SEQ ID NO. 326.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 327, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-1326 of SEQ ID NO. 339, which also
corresponds to amino acids 1-1326 of SEQ ID NO. 327, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 1327-1336 of SEQ ID NO. 327, wherein
said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 327, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VRPSGEGGQA (SEQ ID NO:431) in SEQ ID NO. 327.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 328, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-1508 of SEQ ID NO.
339, which also corresponds to amino acids 1-1508 of SEQ ID NO.
328, and a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1509-1534 of SEQ
ID NO. 328, wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 328, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence GVLGVQEARDELVGGRAMQGQGEHRL (SEQ ID NO:432) in SEQ
ID NO. 328.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 329, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-1763 of SEQ ID NO.
338, which also corresponds to amino acids 1-1763 of SEQ ID NO.
329, and a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1764-1788 of SEQ
ID NO. 329, wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 329, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VSDRPPSASPKDRNKALGPGQATVL (SEQ ID NO:432) in SEQ ID
NO. 329.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 330, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1-22 of SEQ ID
NO. 330, and a second amino acid sequence being at least 90%
homologous to amino acids 528-1939 of SEQ ID NO. 340, which also
corresponds to amino acids 23-1434 of SEQ ID NO. 330, wherein said
first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 330, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MGLWKPGSVLSDSLFASSPCPQ (SEQ ID NO:395) of SEQ ID
NO. 330.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 331, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-527 of SEQ ID NO. 339, which also
corresponds to amino acids 1-527 of SEQ ID NO. 331, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 528-555 of SEQ ID NO. 331, wherein
said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 331, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VPPWPHHLCPLLCHPDKVVAESLLHPRN (SEQ ID NO:435) in SEQ
ID NO. 331.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO.332, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-470 of SEQ ID NO.338,
which also corresponds to amino acids 1-470 of SEQ ID NO.332, a
second amino acid sequence being at least 90% homologous to amino
acids 528-1855 of SEQ ID NO.338, which also corresponds to amino
acids 471-1798 of SEQ ID NO.332, and a third amino acid sequence
being at least 70%, optionally at least 80%, preferably at least
85%, more preferably at least 90% and most preferably at least 95%
homologous to a polypeptide sequence corresponding to amino acids
1799-1847 of SEQ ID NO.332, wherein said first amino acid sequence,
second amino acid sequence and third amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for an edge
portion of SEQ ID NO.332, comprising a polypeptide having a length
"n", wherein n is at least about 10 amino acids in length,
optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least
about 40 amino acids in length and most preferably at least about
50 amino acids in length, wherein at least two amino acids comprise
DP, having a structure as follows: a sequence starting from any of
amino acid numbers 470-x to 470; and ending at any of amino acid
numbers 471+((n-2)-x), in which x varies from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 332, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VRRTPDTGSRCGSFFSGPTAPPSQGSSHLLLEMLLVDLTFFSRSAVSLT
(SEQ ID NO:394) in SEQ ID NO.332.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO.333, comprising a first amino acid sequence being at least 90%
homologous to amino acids 165-1939 of SEQ ID NO. 340, which also
corresponds to amino acids 1-1775 of SEQ ID NO.333.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO.334, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1165-1939 of SEQ ID NO.
340, which also corresponds to amino acids 1-775 of SEQ ID
NO.334.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO.317, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-158 of SEQ ID NO. 341, which also
corresponds to amino acids 1-158 of SEQ ID NO.317.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO.318, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-156 of SEQ ID NO. 341, which also
corresponds to amino acids 1-156 of SEQ ID NO.318, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 157-166 of SEQ ID NO.318, wherein said
first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO.318, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VSVGQECGSG (SEQ ID NO:423) in SEQ ID NO.318.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO.319, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-156 of SEQ ID NO. 341, which also
corresponds to amino acids 1-156 of SEQ ID NO.319, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 157-210 of SEQ ID NO.319, wherein said
first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO.319, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence
DGISSLCYSSLSKSLLSQPLRETSSAINDISLLQALMPLLGWTSHWTCITVGLY (SEQ ID
NO:424) in SEQ ID NO.319.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 320, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-60 of Q96NR4 (SEQ ID NO:342), which
also corresponds to amino acids 1-60 of SEQ ID NO. 320, and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 61-114 of SEQ ID NO. 320, wherein said
first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 320, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence
DGISSLCYSSLSKSLLSQPLRETSSAINDISLLQALMPLLGWTSHWTCITVGLY (SEQ ID
NO:424) in SEQ ID NO. 320.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 320, comprising a first amino acid sequence being at least 90%
homologous to amino acids 97-156 of SEQ ID NO. 341, which also
corresponds to amino acids 1-60 of SEQ ID NO. 320, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 61-114 of SEQ ID NO. 320, wherein said
first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 321, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-14 of SEQ ID NO. 342, which also
corresponds to amino acids 1-14 of SEQ ID NO. 321, a second amino
acid sequence bridging amino acid sequence comprising of S, and a
third amino acid sequence being at least 90% homologous to
corresponding to amino acids 62-133 of SEQ ID NO. 342, which also
corresponds to amino acids 16-87 of SEQ ID NO. 321, wherein said
first amino acid sequence, second amino acid sequence and third
amino acid sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for an edge portion of
SEQ ID NO. 321, comprising a polypeptide having a length "n",
wherein n is at least about 10 amino acids in length, optionally at
least about 20 amino acids in length, preferably at least about 30
amino acids in length, more preferably at least about 40 amino
acids in length and most preferably at least about 50 amino acids
in length, wherein at least three amino acids comprise VSI having a
structure as follows (numbering according to SEQ ID NO. 321): a
sequence starting from any of amino acid numbers 14-x to 14; and
ending at any of amino acid numbers 16+((n-2)-x), in which x varies
from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 321, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1-15 of SEQ ID
NO. 321, and a second amino acid sequence being at least 90%
homologous to corresponding to amino acids 39-110 of SEQ ID NO.
343, which also corresponds to amino acids 16-87 of SEQ ID NO. 321,
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 321, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MRGEHNSTSYDSAVS (SEQ ID NO:426) of SEQ ID NO.
321.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 321, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 97-110 of SEQ ID NO.
341, which also corresponds to amino acids 1-14 of SEQ ID NO. 321,
a second amino acid sequence bridging amino acid sequence
comprising of S, and a third amino acid sequence being at least 90%
homologous to corresponding to amino acids 158-229 of SEQ ID NO.
341, which also corresponds to amino acids 16-87 of SEQ ID NO. 321,
wherein said first amino acid sequence, second amino acid sequence
and third amino acid sequence are contiguous and in a sequential
order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for an edge portion of
SEQ ID NO. 321, comprising a polypeptide having a length "n",
wherein n is at least about 10 amino acids in length, optionally at
least about 20 amino acids in length, preferably at least about 30
amino acids in length, more preferably at least about 40 amino
acids in length and most preferably at least about 50 amino acids
in length, wherein at least three amino acids comprise VSI having a
structure as follows (numbering according to SEQ ID NO. 321): a
sequence starting from any of amino acid numbers 14-x to 14; and
ending at any of amino acid numbers 16+((n-2)-x), in which x varies
from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 320, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence
DGISSLCYSSLSKSLLSQPLRETSSAINDISLLQALMPLLGWTSHWTCITVGLY (SEQ ID
NO:424) in SEQ ID NO. 320.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 321, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-14 of SEQ ID NO. 342,
which also corresponds to amino acids 1-14 of SEQ ID NO. 321, a
second amino acid sequence bridging amino acid sequence comprising
of S, and a third amino acid sequence being at least 90% homologous
to corresponding to amino acids 62-133 of SEQ ID NO. 342, which
also corresponds to amino acids 16-87 of SEQ ID NO. 321, wherein
said first amino acid sequence, second amino acid sequence and
third amino acid sequence are contiguous and in a sequential
order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for an edge portion of
SEQ ID NO. 321, comprising a polypeptide having a length "n",
wherein n is at least about 10 amino acids in length, optionally at
least about 20 amino acids in length, preferably at least about 30
amino acids in length, more preferably at least about 40 amino
acids in length and most preferably at least about 50 amino acids
in length, wherein at least three amino acids comprise VSI having a
structure as follows (numbering according to SEQ ID NO. 321: a
sequence starting from any of amino acid numbers 14-x to 14; and
ending at any of amino acid numbers 16+((n-2)-x), in which x varies
from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 321, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1-15 of SEQ ID
NO. 321, and a second amino acid sequence being at least 90%
homologous to corresponding to amino acids 39-110 of SEQ ID NO.
343, which also corresponds to amino acids 16-87 of SEQ ID NO. 321,
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 321, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MRGEHNSTSYDSAVS (SEQ ID NO:426) of SEQ ID NO.
321.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 321, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 97-110 of SEQ ID NO.
341, which also corresponds to amino acids 1-14 of SEQ ID NO. 321,
a second amino acid sequence bridging amino acid sequence
comprising of S, and a third amino acid sequence being at least 90%
homologous to corresponding to amino acids 158-229 of SEQ ID NO.
341, which also corresponds to amino acids 16-87 of SEQ ID NO. 321,
wherein said first amino acid sequence, second amino acid sequence
and third amino acid sequence are contiguous and in a sequential
order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for an edge portion of
SEQ ID NO. 321, comprising a polypeptide having a length "n",
wherein n is at least about 10 amino acids in length, optionally at
least about 20 amino acids in length, preferably at least about 30
amino acids in length, more preferably at least about 40 amino
acids in length and most preferably at least about 50 amino acids
in length, wherein at least three amino acids comprise VSI having a
structure as follows (numbering according to SEQ ID NO. 321): a
sequence starting from any of amino acid numbers 14-x to 14; and
ending at any of amino acid numbers 16+((n-2)-x), in which x varies
from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 322, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-62 of SEQ ID NO. 342,
which also corresponds to amino acids 1-62 of SEQ ID NO. 322.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 322, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1-23 of SEQ ID
NO. 322, and a second amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-39 of SEQ ID NO. 343,
which also corresponds to amino acids 24-62 of SEQ ID NO. 322,
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 322, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MRGEHNSTSYDSAVIYRGFWAVL (SEQ ID NO:427) of SEQ ID
NO. 322.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 322, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 97-158 of SEQ ID NO.
341, which also corresponds to amino acids 1-62 of SEQ ID NO.
322.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 324, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-60 of SEQ ID NO. 342,
which also corresponds to amino acids 1-60 of SEQ ID NO. 324, and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 61-70 of SEQ ID NO. 324, wherein said
first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 324, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VSVGQECGSG (SEQ ID NO:423) in SEQ ID NO. 324.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 324, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1-23 of SEQ ID
NO. 324, a second amino acid sequence being at least 90% homologous
to corresponding to amino acids 1-37 of SEQ ID NO. 343, which also
corresponds to amino acids 24-60 of SEQ ID NO. 324, and a third
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence corresponding to amino acids 61-70 of SEQ ID NO. 324,
wherein said first amino acid sequence, second amino acid sequence
and third amino acid sequence are contiguous and in a sequential
order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 324, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MRGEHNSTSYDSAVIYRGFWAVL (SEQ ID NO:427) of SEQ ID
NO. 324.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 324, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VSVGQECGSG (SEQ ID NO:423) in SEQ ID NO. 324.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 324, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 97-156 of SEQ ID NO.
341, which also corresponds to amino acids 1-60 of SEQ ID NO. 324,
and a second amino acid sequence being at least 70%, optionally at
least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide having
the sequence corresponding to amino acids 61-70 of SEQ ID NO. 324,
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 324, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VSVGQECGSG (SEQ ID NO:423) in SEQ ID NO. 324.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 313, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-115 of SEQ ID NO. 344,
which also corresponds to amino acids 1-115 of SEQ ID NO. 313, and
a second amino acid sequence being at least 90% homologous to
corresponding to amino acids 152-319 of SEQ ID NO. 344, which also
corresponds to amino acids 116-283 of SEQ ID NO. 313, wherein said
first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for an edge
portion of SEQ ID NO. 313, comprising a polypeptide having a length
"n", wherein n is at least about 10 amino acids in length,
optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least
about 40 amino acids in length and most preferably at least about
50 amino acids in length, wherein at least two amino acids comprise
IY, having a structure as follows: a sequence starting from any of
amino acid numbers 115-x to 115; and ending at any of amino acid
numbers 116+((n-2)-x), in which x varies from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 313, of cluster Z36249 comprising a first amino acid sequence
being at least 90% homologous to corresponding to amino acids 1-70
of SEQ ID NO. 345, which also corresponds to amino acids 1-70 of
SEQ ID NO. 313, a bridging amino acid K corresponding to amino acid
71 of SEQ ID NO. 313, a second amino acid sequence being at least
90% homologous to corresponding to amino acids 72-115 of SEQ ID NO.
345, which also corresponds to amino acids 72-115 of SEQ ID NO.
313, and a third amino acid sequence being at least 90% homologous
to corresponding to amino acids 152-319 of SEQ ID NO. 345, which
also corresponds to amino acids 116-283 of SEQ ID NO. 313, wherein
said first amino acid sequence, bridging amino acid, second amino
acid sequence and third amino acid sequence are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 314, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-184 of SEQ ID NO. 344,
which also corresponds to amino acids 1-184 of SEQ ID NO. 314, and
a second amino acid sequence being at least 70%, optionally at
least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide
sequence corresponding to amino acids 185-197 of SEQ ID NO. 314,
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 314, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VNIFLCLGMSQKK (SEQ ID NO:421) in SEQ ID NO.
314.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 314, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-70 of SEQ ID NO. 345,
which also corresponds to amino acids 1-70 of SEQ ID NO. 314, a
bridging amino acid K corresponding to amino acid 71 of SEQ ID NO.
314, a second amino acid sequence being at least 90% homologous to
corresponding to amino acids 72-184 of SEQ ID NO. 345, which also
corresponds to amino acids 72-184 of SEQ ID NO. 314, and a third
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence corresponding to amino acids 185-197 of SEQ ID NO. 314,
wherein said first amino acid sequence, bridging amino acid, second
amino acid sequence and third amino acid sequence are contiguous
and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 314, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VNIFLCLGMSQKK (SEQ ID NO:421) in SEQ ID NO.
314.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for an edge
portion of SEQ ID NO. 313, comprising a polypeptide having a length
"n", wherein n is at least about 10 amino acids in length,
optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least
about 40 amino acids in length and most preferably at least about
50 amino acids in length, wherein at least two amino acids comprise
IY, having a structure as follows: a sequence starting from any of
amino acid numbers 115-x to 115; and ending at any of amino acid
numbers 116+((n-2)-x), in which x varies from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 315, comprising a first amino acid sequence being at least 90%
homologous to corresponding to amino acids 1-151 of SEQ ID NO. 344,
which also corresponds to amino acids 1-151 of SEQ ID NO. 315, and
a second amino acid sequence being at least 70%, optionally at
least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide
sequence corresponding to amino acids 152-177 of SEQ ID NO. 315,
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 315, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VRLMQSTAKSSSLILCFLCFTPVLLI (SEQ ID NO:422) in SEQ
ID NO. 315.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 315, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-70 of SEQ ID NO. 345, which also
corresponds to amino acids 1-70 of SEQ ID NO. 315, a bridging amino
acid K corresponding to amino acid 71 of SEQ ID NO. 315, a second
amino acid sequence being at least 90% homologous to amino acids
72-151 of SEQ ID NO. 345, which also corresponds to amino acids
72-151 of SEQ ID NO. 315, and a third amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide sequence corresponding to amino acids 152-177 of
SEQ ID NO. 315, wherein said first amino acid sequence, bridging
amino acid, second amino acid sequence and third amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 315, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VRLMQSTAKSSSLILCFLCFTPVLLI (SEQ ID NO:422) in SEQ
ID NO. 315.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 316, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-151 of SEQ ID NO. 344, which also
corresponds to amino acids 1-151 of SEQ ID NO. 316, and a second
amino acid sequence being at least 90% homologous to amino acids
185-319 of SEQ ID NO. 344, which also corresponds to amino acids
152-286 of SEQ ID NO. 316, wherein said first amino acid sequence
and second amino acid sequence are contiguous and in a sequential
order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for an edge
portion of SEQ ID NO. 316, comprising a polypeptide having a length
"n", wherein n is at least about 10 amino acids in length,
optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least
about 40 amino acids in length and most preferably at least about
50 amino acids in length, wherein at least two amino acids comprise
EL, having a structure as follows: a sequence starting from any of
amino acid numbers 151-x to 151; and ending at any of amino acid
numbers 152+((n-2)-x), in which x varies from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 316, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-70 of SEQ ID NO. 345, which also
corresponds to amino acids 1-70 of SEQ ID NO. 316, a bridging amino
acid K corresponding to amino acid 71 of SEQ ID NO. 316, a second
amino acid sequence being at least 90% homologous to amino acids
72-151 of SEQ ID NO. 345, which also corresponds to amino acids
72-151 of SEQ ID NO. 316, and a third amino acid sequence being at
least 90% homologous to amino acids 185-319 of SEQ ID NO. 345,
which also corresponds to amino acids 152-286 of SEQ ID NO. 316,
wherein said first amino acid sequence, bridging amino acid, second
amino acid sequence and third amino acid sequence are contiguous
and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for an edge
portion of SEQ ID NO. 316, of cluster Z36249 comprising a
polypeptide having a length "n", wherein n is at least about 10
amino acids in length, optionally at least about 20 amino acids in
length, preferably at least about 30 amino acids in length, more
preferably at least about 40 amino acids in length and most
preferably at least about 50 amino acids in length, wherein at
least two amino acids comprise EL, having a structure as follows: a
sequence starting from any of amino acid numbers 151-x to 151; and
ending at any of amino acid numbers 152+((n-2)-x), in which x
varies from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 309, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-42 of SEQ ID NO. 346, which also
corresponds to amino acids 1-42 of SEQ ID NO. 309, a bridging amino
acid N corresponding to amino acid 43 of SEQ ID NO. 309, a second
amino acid sequence being at least 90% homologous to amino acids
44-657 of SEQ ID NO. 346, which also corresponds to amino acids
44-657 of SEQ ID NO. 309, and a third amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide sequence corresponding to amino acids 658-708 of
SEQ ID NO. 309, wherein said first amino acid sequence, bridging
amino acid, second amino acid sequence and third amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 309, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VRPHLTLKAPLGLRMHRDPLRTPSPKSWPLTQPLTPDATLTPQAILTPTLT
(SEQ ID NO:418) in SEQ ID NO. 309.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 310, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-42 of SEQ ID NO. 346, which also
corresponds to amino acids 1-42 of SEQ ID NO. 310, a bridging amino
acid N corresponding to amino acid 43 of SEQ ID NO. 310, a second
amino acid sequence being at least 90% homologous to amino acids
44-676 of SEQ ID NO. 346, which also corresponds to amino acids
44-676 of SEQ ID NO. 310, and a third amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide sequence corresponding to amino acids 677-685 of
SEQ ID NO. 310, wherein said first amino acid sequence, bridging
amino acid, second amino acid sequence and third amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 310, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence EHGRGPGKT (SEQ ID NO:419) in SEQ ID NO. 310.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 311, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-42 of SEQ ID NO. 346, which also
corresponds to amino acids 1-42 of SEQ ID NO. 311, a bridging amino
acid N corresponding to amino acid 43 of SEQ ID NO. 311, a second
amino acid sequence being at least 90% homologous to amino acids
44-657 of SEQ ID NO. 346, which also corresponds to amino acids
44-657 of SEQ ID NO. 311, and a third amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide sequence corresponding to amino acids 658-696 of
SEQ ID NO. 311, wherein said first amino acid sequence, bridging
amino acid, second amino acid sequence and third amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 311, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence GPGRHAGNAGTLTQSLDCDAGVPPPAFQPLSTSYIYFSE (SEQ ID
NO:420) in SEQ ID NO. 311.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 312, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-42 of SEQ ID NO. 346, which also
corresponds to amino acids 1-42 of SEQ ID NO. 312, a bridging amino
acid N corresponding to amino acid 43 of SEQ ID NO. 312, a second
amino acid sequence being at least 90% homologous to amino acids
44-610 of SEQ ID NO. 346, which also corresponds to amino acids
44-610 of SEQ ID NO. 312, and a third amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide having the sequence AMH corresponding to amino
acids 611-613 of SEQ ID NO. 312, wherein said first amino acid
sequence, bridging amino acid, second amino acid sequence and third
amino acid sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 305, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-381 of SEQ ID NO. 347, which also
corresponds to amino acids 1-381 of SEQ ID NO. 305, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 382-387 of SEQ ID NO. 305, wherein
said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 305, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence TSLSLS (SEQ ID NO:415) in SEQ ID NO. 305.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 306, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-338 of SEQ ID NO. 347, which also
corresponds to amino acids 1-338 of SEQ ID NO. 306, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 339-346 of SEQ ID NO. 306, wherein
said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 306, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VLLCAQWP (SEQ ID NO:416) in SEQ ID NO. 306.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 307, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-223 of SEQ ID NO. 347, which also
corresponds to amino acids 1-223 of SEQ ID NO. 307, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence A corresponding to amino acids 224-224 of SEQ ID NO. 307,
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 308, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-294 of SEQ ID NO. 347, which also
corresponds to amino acids 1-294 of SEQ ID NO. 308, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 295-304 of SEQ ID NO. 308, wherein
said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 308, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence RCYLRFLDIY (SEQ ID NO:417) in SEQ ID NO. 308.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 281, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a amino
acids 1-116 of FABH_HUMAN (SEQ ID NO:348), which also corresponds
to amino acids 1-116 of SEQ ID NO. 281, and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide sequence corresponding to
amino acids 117-215 of SEQ ID NO. 281, wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 281, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence
VRWATLELYLIGYYYCSFSQACSKKPSPPLRAVEAGTREWLWVRVVSGGNFLCSGFGL
TQAGTQILPYRLHDCGQITFSKCNCKTGINNTNLVGLLGSL (SEQ ID NO:396) in SEQ ID
NO. 281.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 281, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-116 of AAP35373 (SEQ ID NO:348), which
also corresponds to amino acids 1-116 of SEQ ID NO. 281, and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 117-215 of SEQ ID NO. 281, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 281, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence
VRWATLELYLIGYYYCSFSQACSKKPSPPLRAVEAGTREWLWVRVVSGGNFLCSGFGL
TQAGTQILPYRLHDCGQITFSKCNCKTGINNTNLVGLLGSL (SEQ ID NO:396) in SEQ ID
NO. 281.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 282, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1-116 of
FABH_HUMAN (SEQ ID NO:348), which also corresponds to amino acids
1-116 of SEQ ID NO. 282, and a second amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide sequence corresponding to amino acids 117-178 of
SEQ ID NO. 282, wherein said first and second amino acid sequences
are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 282, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence
DVLTAWPSIYRRQVKVLREDEITILPWHLQWSREKATKLLRPTLPSYNNHGWEELRVG KSIV
(SEQ ID NO:397) in SEQ ID NO. 282.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 282, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-116 of AAP35373 (SEQ ID NO:348), which
also corresponds to amino acids 1-116 of SEQ ID NO. 282, and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 117-178 of SEQ ID NO. 282, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 282, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence
DVLTAWPSIYRRQVKVLREDEITILPWHLQWSREKATKLLRPTLPSYNNHGWEELRVG KSIV
(SEQ ID NO:397) in SEQ ID NO. 282.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 283, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence amino acids 1-116 of FABH_HUMAN
(SEQ ID NO:348), which also corresponds to amino acids 1-116 of SEQ
ID NO. 283, and a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 117-126 of SEQ ID
NO. 283, wherein said first and second amino acid sequences are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 283, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MEKLQLRNVK (SEQ ID NO:398) in SEQ ID NO. 283.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 283, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-116 of AAP35373 (SEQ ID NO:348), which
also corresponds to amino acids SEQ ID NO. 283, and a second amino
acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 117-126 of SEQ ID NO. 283, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 283, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MEKLQLRNVK (SEQ ID NO:398) in SEQ ID NO. 283.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 284, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-24 of FABH_HUMAN (SEQ ID NO:348), which
also corresponds to amino acids 1-24 of SEQ ID NO. 284, second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 25-35 of SEQ ID NO. 284, and a third
amino acid sequence being at least 90% homologous to amino acids
25-133 of FABH_HUMAN (SEQ ID NO:348), which also corresponds to
amino acids 36-144 of SEQ ID NO. 284, wherein said first, second,
third and fourth amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for an edge portion of
SEQ ID NO. 284, comprising an amino acid sequence being at least
70%, optionally at least about 80%, preferably at least about 85%,
more preferably at least about 90% and most preferably at least
about 95% homologous to the sequence encoding for AHILITFPLPS (SEQ
ID NO:399), corresponding to SEQ ID NO. 284.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 284, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-24 of AAP35373 (SEQ ID NO:348), which
also corresponds to amino acids 1-24 of SEQ ID NO. 284, second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 25-35 of SEQ ID NO. 284, and a third
amino acid sequence being at least 90% homologous to amino acids
25-133 of AAP35373 (SEQ ID NO:348), which also corresponds to amino
acids 36-144 of SEQ ID NO. 284, wherein said first, second and
third amino acid sequences are contiguous and in a sequential
order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for an edge portion of
SEQ ID NO. 284, comprising an amino acid sequence being at least
70%, optionally at least about 80%, preferably at least about 85%,
more preferably at least about 90% and most preferably at least
about 95% homologous to the sequence encoding for AHILITFPLPS (SEQ
ID NO:399), corresponding to SEQ ID NO. 284.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 285, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-203 of SEQ ID NO. 349, which also
corresponds to amino acids 1-203 of SEQ ID NO. 285, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 204-240 of SEQ ID NO. 285, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 285, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence LWLTPVIPTLWEADGGGLHEPWSWRPAWATWLQRNYL (SEQ ID
NO:400) in SEQ ID NO. 285.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 286, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-78 of SEQ ID NO. 349, which also
corresponds to amino acids 1-78 of SEQ ID NO. 286, second amino
acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 79-125 of SEQ ID NO. 286, and a third
amino acid sequence being at least 90% homologous to amino acids
79-399 of SEQ ID NO. 349, which also corresponds to amino acids
126-446 of SEQ ID NO. 286, wherein said first, second and third
amino acid sequences are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for an edge portion of
SEQ ID NO. 286, comprising an amino acid sequence being at least
70%, optionally at least about 80%, preferably at least about 85%,
more preferably at least about 90% and most preferably at least
about 95% homologous to the sequence encoding for
HWQISQWWLHFQTPREEGKMKLLELSESADGAAWKRWGGNSNTHRIQ (SEQ ID NO:401),
corresponding to SEQ ID NO. 286.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 287, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-140 of SEQ ID NO. 349, which also
corresponds to amino acids 1-140 of SEQ ID NO. 287, and a second
amino acid sequence being at least 90% homologous to amino acids
203-399 of SEQ ID NO. 349, which also corresponds to amino acids
141-337 of SEQ ID NO. 287, wherein said first and second amino acid
sequences are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for an edge
portion of SEQ ID NO. 287, comprising a polypeptide having a length
"n", wherein "n" is at least about 10 amino acids in length,
optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least
about 40 amino acids in length and most preferably at least about
50 amino acids in length, wherein at least two amino acids comprise
DV, having a structure as follows: a sequence starting from any of
amino acid numbers 140-x to 140; and ending at any of amino acid
numbers 141+((n-2)-x), in which x varies from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 288, comprising a
first amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 1-10 of SEQ ID NO. 288, second amino
acid sequence being at least 90% homologous to amino acids 18-106
of SEQ ID NO. 349, which also corresponds to amino acids 11-99 of
SEQ ID NO. 288, a third (bridging) amino acid sequence comprising
D, and a fourth amino acid sequence being at least 90% homologous
to amino acids 179-399 of SEQ ID NO. 349, which also corresponds to
amino acids 101-321 of SEQ ID NO. 288, wherein said first, second,
third and fourth amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 288, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence NETEAEQSYV (SEQ ID NO:402) of SEQ ID NO. 288.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for an edge portion of
SEQ ID NO. 288, comprising a polypeptide having a length "n",
wherein "n" is at least about 10 amino acids in length, optionally
at least about 20 amino acids in length, preferably at least about
30 amino acids in length, more preferably at least about 40 amino
acids in length and most preferably at least about 50 amino acids
in length, wherein at least two amino acids comprise LDY having a
structure as follows (numbering according to SEQ ID NO. 288): a
sequence starting from any of amino acid numbers 99-x to 99; and
ending at any of amino acid numbers 101+((n-2)-x), in which x
varies from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 289, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1-15 of SEQ ID
NO. 289, and a second amino acid sequence being at least 90%
homologous to corresponding to amino acids 203-399 of SEQ ID NO.
349, which also corresponds to amino acids 16-212 of SEQ ID NO.
289, wherein said first and second amino acid sequences are
contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 289, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MSSWLSAGSPSSLSV (SEQ ID NO:403) of SEQ ID NO.
289.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 290, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1-13 of SEQ ID
NO. 290, and a second amino acid sequence being at least 90%
homologous to amino acids 280-399 of SEQ ID NO. 349, which also
corresponds to amino acids 14-133 of SEQ ID NO. 290, wherein said
first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 290, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MCRGYSTLLNPVS (SEQ ID NO:404) of SEQ ID NO.
290.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 291, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-246 of SEQ ID NO. 349, which also
corresponds to amino acids 1-246 of SEQ ID NO. 291, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 247-252 of SEQ ID NO. 291, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 291, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence SRNWTQ (SEQ ID NO:405) in SEQ ID NO. 291.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 292, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide sequence corresponding to amino acids 1-10 of SEQ ID
NO. 292, second amino acid sequence being at least 90% homologous
to amino acids 26-276 of Q96NF5 (SEQ ID NO:362), which also
corresponds to amino acids 11-261 of SEQ ID NO. 292, followed by A,
and a third amino acid sequence being at least 90% homologous to
amino acids 278-466 of Q96NF5 (SEQ ID NO:362), which also
corresponds to amino acids 263-451 of SEQ ID NO. 292, wherein said
first, second, A, and third amino acid sequences are contiguous and
in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 292, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MEISLVKCSE (SEQ ID NO:406) of SEQ ID NO. 292
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 293, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-276 of Q96NF5 (SEQ ID NO:362), which
also corresponds to amino acids 1-276 of SEQ ID NO. 293, followed
by A, a second amino acid sequence being at least 90% homologous to
amino acids 278-372 of Q96NF5 (SEQ ID NO:362), which also
corresponds to amino acids 278-372 of SEQ ID NO. 293, and a third
amino acid sequence being at least 90% homologous to amino acids
401-466 of Q96NF5 (SEQ ID NO:362), which also corresponds to amino
acids 373-438 of SEQ ID NO. 293, wherein said first, A, second, and
third amino acid sequences are contiguous and in a sequential
order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for an edge
portion of SEQ ID NO. 293, comprising a polypeptide having a length
"n", wherein n is at least about 10 amino acids in length,
optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least
about 40 amino acids in length and most preferably at least about
50 amino acids in length, wherein at least two amino acids comprise
EE, having a structure as follows: a sequence starting from any of
amino acid numbers 372-x to 372; and ending at any of amino acid
numbers 373+((n-2)-x), in which x varies from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 294, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-276 of Q96NF5 (SEQ ID NO:362), which
also corresponds to amino acids 1-276 of SEQ ID NO. 294, followed
by A, a second amino acid sequence being at least 90% homologous to
amino acids 278-401 of Q96NF5 (SEQ ID NO:362), which also
corresponds to amino acids 278-401 of SEQ ID NO. 294, and a third
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 402-407 of SEQ ID NO. 294, wherein
said first, A, second and third amino acid sequences are contiguous
and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 294, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence PNRQDS (SEQ ID NO:407) in SEQ ID NO. 294.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 295, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-276 of Q96NF5 (SEQ ID NO:362), which
also corresponds to amino acids 1-276 of SEQ ID NO. 295, followed
by A, a second amino acid sequence being at least 90% homologous to
amino acids 278-374 of Q96NF5 (SEQ ID NO:362), which also
corresponds to amino acids 278-374 of SEQ ID NO. 295, and a third
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 375-390 of SEQ ID NO. 295, wherein
said first, A, second and third amino acid sequences are contiguous
and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 295, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MSHELFSRFSLRLFGR (SEQ ID NO:408) in SEQ ID NO.
295.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 296, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-261 of Q96NF5 (SEQ ID NO:362), which
also corresponds to amino acids 1-261 of SEQ ID NO. 296, a second
amino acid sequence comprising A, and a third amino acid sequence
being at least 90% homologous to amino acids 263-451 of Q96NF5 (SEQ
ID NO:362), which also corresponds to amino acids 263-451 of SEQ ID
NO. 296, wherein said first, second and third amino acid sequences
are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 297, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-132 of Q9NPI5 (SEQ ID NO:372), which
also corresponds to amino acids 1-132 of SEQ ID NO. 297, and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 133-145 of SEQ ID NO. 297, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 297, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence LPGRHEVPRGALP (SEQ ID NO:409) in SEQ ID NO.
297.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 297, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-109 of Q9NZK3 (SEQ ID NO:373), which
also corresponds to amino acids 1-109 of SEQ ID NO. 297, and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 110-145 of SEQ ID NO. 297, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 297, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence LVDLYSRRYFLTVPYEECKWRRSLPGRHEVPRGALP in SEQ ID NO.
297.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 298, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-107 of Q9NPI5 (SEQ ID NO:372), which
also corresponds to amino acids 1-107 of SEQ ID NO. 298, and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 108-121 of SEQ ID NO. 298, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 298, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence NLPGRHEVPRGALP (SEQ ID NO:410) in SEQ ID NO.
298.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 298, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-107 of Q9NZK3 (SEQ ID NO:373), which
also corresponds to amino acids 1-107 of SEQ ID NO. 298, and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 108-121 of SEQ ID NO. 298, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 298, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence NLPGRHEVPRGALP (SEQ ID NO:410) in SEQ ID NO.
298.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 299, comprising a first amino acid sequence being at least 90%
homologous to amino acids 51-151 of SEQ ID NO. 350, which also
corresponds to amino acids 1-101 of SEQ ID NO. 299.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 300, comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence MSSFSTTT (SEQ ID NO:411)
corresponding to amino acids 1-8 of SEQ ID NO. 300, and a second
amino acid sequence being at least 90% homologous to amino acids
42-151 of SEQ ID NO. 350, which also corresponds to amino acids
9-118 of SEQ ID NO. 300, wherein said first and second amino acid
sequences are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a head of SEQ ID
NO. 300, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MSSFSTTT (SEQ ID NO:411) of SEQ ID NO. 300.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 301, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-124 of TRIC_HUMAN, which also
corresponds to amino acids 1-124 of SEQ ID NO. 301, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 125-137 of SEQ ID NO. 301, wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 301, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VGRMGSSGTFGVG (SEQ ID NO:412) in SEQ ID NO.
301.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 302, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-8 of TRIC_HUMAN, which also corresponds
to amino acids 1-8 of SEQ ID NO. 302, and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide sequence corresponding to
amino acids 36-209 of TRIC_HUMAN, which also corresponding to amino
acids 9-182 of SEQ ID NO. 302, wherein said first and second amino
acid sequences are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for an edge
portion of SEQ ID NO. 302, comprising a polypeptide having a length
"n", wherein "n" is at least about 10 amino acids in length,
optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least
about 40 amino acids in length and most preferably at least about
50 amino acids in length, wherein at least two amino acids comprise
AK, having a structure as follows: a sequence starting from any of
amino acid numbers 8-x to 8; and ending at any of amino acid
numbers 9+((n-2)-x), in which x varies from 0 to n-2.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 303, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-36 of TRIC_HUMAN, which also
corresponds to amino acids 1-36 of SEQ ID NO. 303, and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide sequence
corresponding to amino acids 37-86 of SEQ ID NO. 303, wherein said
first and second amino acid sequences are contiguous and in a
sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 303, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VGRGFLGAEYRRRRDPRPWEWGEEPGLRRGRGLRGGASGAEFCRGSCSDW
(SEQ ID NO:413) in SEQ ID NO. 303.
According to preferred embodiments of the present invention, there
is provided an isolated chimeric polypeptide encoding for SEQ ID
NO. 304, comprising a first amino acid sequence being at least 90%
homologous to amino acids 1-8 of TRIC_HUMAN, which also corresponds
to amino acids 1-8 of SEQ ID NO. 304, and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide sequence corresponding to
amino acids 9-13 of SEQ ID NO. 304, wherein said first and second
amino acid sequences are contiguous and in a sequential order.
According to preferred embodiments of the present invention, there
is provided an isolated polypeptide encoding for a tail of SEQ ID
NO. 304, comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence VRAAG (SEQ ID NO:414) in SEQ ID NO. 304.
According to preferred embodiments of the present invention, there
is provided an antibody capable of specifically binding to an
epitope of an amino acid sequence in any one of cluster S67314,
N56180, T10377, Z24874, HUMCDDANF, HUMTROPIA, HUMSMCK, H88495,
Z36249, FLJ26352, HSACMHCP. Preferably, the amino acid sequence
corresponds to any insertion, including a bridge, edge portion,
tail, or head as described herein.
Preferably, the antibody is capable of differentiating between a
splice variant having the epitope and a corresponding known
protein.
According to preferred embodiments of the present invention, there
is provided a kit for detecting heart disorders, comprising a kit
detecting overexpression of a splice variant. Optionally, the kit
comprises a NAT-based technology. Preferably, the kit further
comprises at least one primer pair capable of selectively
hybridizing to a nucleic acid sequence in any one of cluster
S67314, N56180, T10377, Z24874, HUMCDDANF, HUMTROPIA, HUMSMCK,
H88495, Z36249, FLJ26352, HSACMHCP.
Optionally, the kit further comprises at least one oligonucleotide
capable of selectively hybridizing to a nucleic acid sequence in
any one of cluster S67314, N56180, T10377, Z24874, HUMCDDANF,
HUMTROPIA, HUMSMCK, H88495, Z36249, FLJ26352, HSACMHCP.
Optionally, kit comprises an antibody as described herein.
Preferably, the kit further comprises at least one reagent for
performing an ELISA or a Western blot.
According to preferred embodiments of the present invention, there
is provided a method for detecting heart disorders, comprising
detecting overexpression of a splice variant of any of cluster
S67314, N56180, T10377, Z24874, HUMCDDANF, HUMTROPIA, HUMSMCK,
H88495, Z36249, FLJ26352, HSACMHCP. Optionally, detecting
overexpression is performed with a NAT-based technology.
Also optionally, detecting overexpression is performed with an
immunoassay. Preferably, the immunoassay comprises an antibody as
described herein.
According to preferred embodiments of the present invention, there
is provided a biomarker capable of detecting heart disorders,
comprising any of the above nucleic acid sequences or a fragment
thereof, or amino acid sequences or a fragment thereof.
According to preferred embodiments of the present invention, there
is provided a method for screening for heart disorders, comprising
detecting cardiac disease cells or tissue with a biomarker or an
antibody.
According to preferred embodiments of the present invention, there
is provided a method for diagnosing heart disorders, comprising
detecting heart cells or tissue with a biomarker or an
antibody.
According to preferred embodiments of the present invention, there
is provided a method for monitoring disease progression, or
treatment efficacy, or relapse of heart disorders, or any
combination thereof, comprising detecting heart cells or tissue
with a biomarker or an antibody or a method or assay as described
herein.
According to preferred embodiments of the present invention, there
is provided a method of selecting a therapy for heart disorders,
comprising detecting heart disorder cells with a biomarker or an
antibody or a method or assay as described herein and selecting a
therapy according to the detection.
A heart disorder and/or cardiac disease and/or cardiac pathology
optionally comprises at least one of: Myocardial infarct, ungina
pectoris (stable and unstable), cardiomyopathy, myocarditis,
congestive heart failure, the detection of reinfarction, the
detection of success of thrombolytic therapy after Myocardial
infarct, Myocardial infarct after surgery, assessing the size of
infarct in Myocardial infarct.
According to preferred embodiments of the present invention,
preferably any of the above nucleic acid and/or amino acid
sequences further comprises any sequence having at least about 70%,
preferably at least about 80%, more preferably at least about 90%,
most preferably at least about 95% homology thereto.
All nucleic acid sequences and/or amino acid sequences shown herein
as embodiments of the present invention relate to their isolated
form, as isolated polynucleotides (including for all transcripts),
oligonucleotides (including for all segments, amplicons and
primers), peptides (including for all tails, bridges, insertions or
heads, optionally including other antibody epitopes as described
herein) and/or polypeptides (including for all proteins). It should
be noted that oligonucleotide and polynucleotide, or peptide and
polypeptide, may optionally be used interchangeably.
Unless defined otherwise, all technical and scientific terms used
herein have the meaning commonly understood by a person skilled in
the art to which this invention belongs. The following references
provide one of skill with a general definition of many of the terms
used in this invention: Singleton et al., Dictionary of
Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge
Dictionary of Science and Technology (Walker ed., 1988); The
Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer
Verlag (1991); and Hale & Marham, The Harper Collins Dictionary
of Biology (1991). All of these are hereby incorporated by
reference as if fully set forth herein. As used herein, the
following terms have the meanings ascribed to them unless specified
otherwise.
BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 shows a schematic summary of quantitative real-time PCR
analysis.
FIG. 2 is a histogram showing expression of ESTs in each category,
as "parts per million".
FIGS. 3 & 4 are histograms showing expression of
oligonucleotides in various tissues, prob 205738_s_at (SEQ ID
NO:392) & prob 214285_at (SEQ ID NO:393).
FIG. 5A is a histogram showing specific expression of variant
FABH_HUMAN Fatty acid-binding protein transcripts in heart tissue
samples as opposed to other tissues (SEQ ID NO:63).
FIG. 5B is a histogram showing specific expression of variant
FABH_HUMAN protein transcripts (SEQ ID NO:275).
FIG. 6 is a histrogram showing expression of FABH_HUMAN known
protein transcripts (SEQ ID NO:278).
FIG. 7 is a histogram showing expression of the number of heart
tissue-specific clones in libraries/sequences.
FIG. 8 is a histogram showing the actual expression of
oligonucleotides in various tissues, including heart tissue, prob
207317_s_at (SEQ ID NO:392).
FIG. 9 is a histogram showing specific expression of the
above-indicated Calsequestrin, cardiac muscle isoform transcripts
in sequence N56180, heart tissue samples (SEQ ID NO:335).
FIG. 10 is a histogram showing specific expression of the
above-indicated Calsequestrin, cardiac muscle isoform transcripts
in heart tissue samples as opposed to other tissues (SEQ ID
NO:361).
FIG. 11 is a histogram showing expression of concerning the number
of heart tissue-specific clones in libraries/sequences.
FIG. 12 is a histogram showing specific expression of Q96NF5
transcripts in sequence T10377 in heart tissue samples (SEQ ID
NO:365).
FIG. 13 is a histogram showing specific expression of the Q96NF5
transcripts in sequence T10377 junc29-33 (SEQ ID NO:368) heart
tissue samples.
FIG. 14 is a histogram showing specific expression of the
above-indicated Q96NF5 transcripts T10377 seg2-3 (SEQ ID NO:371) in
heart tissue samples.
FIG. 15 is a histogram concerning the expression of the number of
heart-specific clones in libraries/sequences.
FIG. 16 is a histogram concerning the actual expression of
oligonucleotides in various tissues, prob 221051_s_at (SEQ ID
NO:392), including heart.
FIG. 17A is a histogram concerning the expressions of ESTs in
number of heart tissue-specific clones in libraries/sequences;
FIG. 17B is a histogram concerning the actual expression of
oligonucleotides in various tissues, prob 209957_s-at (SEQ ID
NO:392), including heart tissue.
FIG. 18 is a histogram showing expression of known protein
transcript for HUMCDDANF_T4 (SEQ ID NO:21).
FIG. 19 is a histogram concerning expression of ESTs, the number of
heart tissue-specific clones in libraries/sequences
FIG. 20 is a histogram concerning the actual expression of
oligonucleotides in various tissues, prob 205742_at (SEQ ID
NO:393), including heart tissue.
FIG. 21A is a histogram showing specific expression of the
above-indicated TRIC_HUMAN Troponin I, cardiac muscle HUMTROPIA
transcripts in sequence HUMTROPIA seg10 in heart tissue (SEQ ID
NO:379).
FIG. 21A is a histogram showing specific expression of the
TRIC_HUMAN Troponin I, cardiac muscle HUMTROPIA transcripts in
sequence HUMTROPIA seg22 in heart tissue (SEQ ID NO:382).
FIG. 22 is a histogram showing specific expression of the HUMTROPIA
known protein sequence in heart tissue.
FIG. 23 is a histogram showing ESTs concerning the number of heart
tissue-specific clones in libraries/sequences FIG. 24 is a
histogram concerning the actual expression of oligonucleotides in
various tissues, pob 205295_at (SEQ ID NO:393), including heart
tissue.
FIG. 25 is a histogram showing ESTs concerning the number of heart
tissue-specific clones in libraries/sequences
FIG. 26 is a histogram concerning the actual expression of
oligonucleotides in various tissues, prob 207066_at (SEQ ID
NO:392), including heart tissue.
FIG. 27 is a histogram showing ESTs concerning the number of
heart-specific clones in libraries/sequences.
FIG. 28 is a histogram concerning the actual expression of
oligonucleotides in various tissues, prob 206029_at (SEQ ID
NO:393), including heart tissue.
FIG. 29 is a histogram concerning expression of ESTs in the number
of heart tissue-specific clones in libraries/sequences.
FIG. 30 is a histogram concerning the expression of ESTs in number
of heart tissue-specific clones in libraries/sequences;
FIG. 31 is a histogram concerning the actual expression of
oligonucleotides in various tissues, prob 204737_s_at (SEQ ID
NO:392), including heart tissue.
FIG. 32 is a histogram concerning the actual expression of
oligonucleotides in various tissues, prob 216265_x_at (SEQ ID
NO:392), including heart tissue.
FIG. 33 shows a diagram of a troponin I variant, HUMTROPIA_T7, with
regard to introducing a mutation to block an additional ORF.
FIG. 34 shows Troponin PCR product after second amplification
reaction: Lane 1: 1 Kb MW marker (GibcoBRL Cat #15615-016) and Lane
2: PCR product.
FIG. 35 shows Troponin PCR product sequence (nucleotides 80-466 of
SEQ ID NO:25).
FIG. 36: plasmid map of His Troponin T7 pRSETA (SEQ ID NO:386).
FIG. 37 shows the complete sequence of the plasmid shown in FIG. 36
(SEQ ID NO:386).
FIG. 38 shows the protein sequence of Troponin variant
HUMTROPIA_PEA.sub.--2 T7, with the HIS-tag marked (SEQ ID
NO:387).
FIG. 39a shows Coomassie staining analysis of SDS-PAGE containing
recombinant HisTroponin; lane 1: Molecular weight marker (ProSieve
color, Cambrex, Cat #50550); lane 2: HisTroponinT7 pRSETA (SEQ ID
NO:386) T0; lane 3: pRSET A T3; lane 4: pRSET empty vector T0
(negative control); lane 5: pRSET empty vector T3 (negative
control).
FIG. 39b shows a Western blot analysis of recombinant HisTroponin:
lane 1: His positive control protein; lane 2: HisTroponinT7 pRSETA
(SEQ ID NO:386) T0; lane 3: HisTroponinT7 pRSETA T3; lane 4: pRSET
empty vector T0 (negative control); lane 5: pRSET empty vector T3
(negative control) and lane 6: molecular weight marker (ProSieve
color, Cambrex, Cat #50550).
DESCRIPTION OF PREFERRED EMBODIMENTS
The present invention is of novel markers for cardiac disease that
are both sensitive and accurate. Biomolecular sequences (amino acid
and/or nucleic acid sequences) uncovered using the methodology of
the present invention and described herein can be efficiently
utilized as tissue or pathological markers and/or as drugs or drug
targets for treating or preventing a disease.
These markers are specifically released to the bloodstream under
conditions of cardiac disease and/or cardiac pathology, including
but not limited to cardiac damage, and/or are otherwise expressed
at a much higher level and/or specifically expressed in heart. The
method of the present invention identifies clusters (genes) which
are characterized in that the transcripts are differentially
expressed in heart muscle tissue compared with other normal
tissues, preferably in comparison to skeletal muscle tissue. In
acute conditions under which heart muscle tissue experiences
hypoxia (with or without necrosis), intracellular proteins that are
not normally secreted can leak through the cell membrane to the
extracellular space. Therefore, heart muscle tissue differentially
expressed proteins, as through analysis of EST expression, are
potential acute heart damage markers.
Leakage of intracellular content can also occur in chronic damage
to the heart muscle, therefore proteins selected according to this
method are potential markers for chronic heart conditions. When a
protein that is differentially expressed in heart muscle is
secreted, it is even more likely to be useful as a chronic heart
damage marker, since secretion implies that the protein has a
physiological role exterior to the cell, and therefore may be used
by the heart muscle to respond to the chronic damage. This
rationale is empirically supported by the non-limiting examples of
the proteins BNP (brain natriuretic peptide) and ANF (atrial
natriuretic factor), which are differentially expressed heart
muscle proteins that are secreted and which were shown to be
markers for congestive heart failure. In addition, BNP and ANF are
not only differentially expressed in heart tissue, they are also
overexpressed dramatically (hundreds of times greater expression)
when heart failure occurs. Other heart specific secreted proteins
might present similar overexpression in chronic damage.
Optionally and preferably, the markers described herein are
overexpressed in heart as opposed to muscle, as described in
greater detail below. The measurement of these markers, alone or in
combination, in patient samples provides information that the
diagnostician can correlate with a probable diagnosis of cardiac
disease and/or cardiac pathology, including but not limited to
cardiac damage.
The present invention therefore also relates to diagnostic assays
for cardiac disease and/or cardiac pathology, including but not
limited to cardiac damage, and methods of use of such markers for
detection of cardiac disease and/or cardiac pathology, including
but not limited to cardiac damage (alone or in combination),
optionally and preferably in a sample taken from a subject
(patient), which is more preferably some type of blood sample.
The present invention therefore also relates to diagnostic assays
for cardiac disease and/or cardiac pathology, including but not
limited to cardiac damage, and methods of use of such markers for
detection of cardiac disease and/or cardiac pathology, including
but not limited to cardiac damage (alone or in combination),
optionally and preferably in a sample taken from a subject
(patient), which is more preferably some type of blood sample.
In another embodiment, the present invention relates to bridges,
tails, heads and/or insertions, and/or analogs, homologs and
derivatives of such peptides. Such bridges, tails, heads and/or
insertions are described in greater detail below with regard to the
Examples.
As used herein a "tail" refers to a peptide sequence at the end of
an amino acid sequence that is unique to a splice variant according
to the present invention. Therefore, a splice variant having such a
tail may optionally be considered as a chimera, in that at least a
first portion of the splice variant is typically highly homologous
(often 100% identical) to a portion of the corresponding known
protein, while at least a second portion of the variant comprises
the tail.
As used herein a "head" refers to a peptide sequence at the
beginning of an amino acid sequence that is unique to a splice
variant according to the present invention. Therefore, a splice
variant having such a head may optionally be considered as a
chimera, in that at least a first portion of the splice variant
comprises the head, while at least a second portion is typically
highly homologous (often 100% identical) to a portion of the
corresponding known protein.
As used herein "an edge portion" refers to a connection between two
portions of a splice variant according to the present invention
that were not joined in the wild type or known protein. An edge may
optionally arise due to a join between the above "known protein"
portion of a variant and the tail, for example, and/or may occur if
an internal portion of the wild type sequence is no longer present,
such that two portions of the sequence are now contiguous in the
splice variant that were not contiguous in the known protein. A
"bridge" may optionally be an edge portion as described above, but
may also include a join between a head and a "known protein"
portion of a variant, or a join between a tail and a "known
protein" portion of a variant, or a join between an insertion and a
"known protein" portion of a variant.
Optionally and preferably, a bridge between a tail or a head or a
unique insertion, and a "known protein" portion of a variant,
comprises at least about 10 amino acids, more preferably at least
about 20 amino acids, most preferably at least about 30 amino
acids, and even more preferably at least about 40 amino acids, in
which at least one amino acid is from the tail/head/insertion and
at least one amino acid is from the "known protein" portion of a
variant. Also optionally, the bridge may comprise any number of
amino acids from about 10 to about 40 amino acids (for example, 10,
11, 12, 13 . . . 37, 38, 39, 40 amino acids in length, or any
number in between).
It should be noted that a bridge cannot be extended beyond the
length of the sequence in either direction, and it should be
assumed that every bridge description is to be read in such manner
that the bridge length does not extend beyond the sequence
itself.
Furthermore, bridges are described with regard to a sliding window
in certain contexts below. For example, certain descriptions of the
bridges feature the following format: a bridge between two edges
(in which a portion of the known protein is not present in the
variant) may optionally be described as follows: a bridge portion
of CONTIG-NAME_P1 (representing the name of the protein),
comprising a polypeptide having a length "n", wherein n is at least
about 10 amino acids in length, optionally at least about 20 amino
acids in length, preferably at least about 30 amino acids in
length, more preferably at least about 40 amino acids in length and
most preferably at least about 50 amino acids in length, wherein at
least two amino acids comprise XX (2 amino acids in the center of
the bridge, one from each end of the edge), having a structure as
follows (numbering according to the sequence of CONTIG-NAME_P1): a
sequence starting from any of amino acid numbers 49-x to 49 (for
example); and ending at any of amino acid numbers 50+((n-2)-x) (for
example), in which x varies from 0 to n-2. In this example, it
should also be read as including bridges in which n is any number
of amino acids between 10-50 amino acids in length. Furthermore,
the bridge polypeptide cannot extend beyond the sequence, so it
should be read such that 49-x (for example) is not less than 1, nor
50+((n-2)-x) (for example) greater than the total sequence
length.
In another embodiment, this invention provides antibodies
specifically recognizing the splice variants and polypeptide
fragments thereof of this invention. Preferably such antibodies
differentially recognize splice variants of the present invention
but do not recognize a corresponding known protein (such known
proteins are discussed with regard to their splice variants in the
Examples below).
In another embodiment, this invention provides an isolated nucleic
acid molecule encoding for a splice variant according to the
present invention, having a nucleotide sequence as set forth in any
one of the sequences listed herein, or a sequence complementary
thereto. In another embodiment, this invention provides an isolated
nucleic acid molecule, having a nucleotide sequence as set forth in
any one of the sequences listed herein, or a sequence complementary
thereto. In another embodiment, this invention provides an
oligonucleotide of at least about 12 nucleotides, specifically
hybridizable with the nucleic acid molecules of this invention. In
another embodiment, this invention provides vectors, cells,
liposomes and compositions comprising the isolated nucleic acids of
this invention.
In another embodiment, this invention provides a method for
detecting a splice variant according to the present invention in a
biological sample, comprising: contacting a biological sample with
an antibody specifically recognizing a splice variant according to
the present invention under conditions whereby the antibody
specifically interacts with the splice variant in the biological
sample but do not recognize known corresponding proteins (wherein
the known protein is discussed with regard to its splice variant(s)
in the Examples below), and detecting said interaction; wherein the
presence of an interaction correlates with the presence of a splice
variant in the biological sample.
In another embodiment, this invention provides a method for
detecting a splice variant nucleic acid sequences in a biological
sample, comprising: hybridizing the isolated nucleic acid molecules
or oligonucleotide fragments of at least about a minimum length to
a nucleic acid material of a biological sample and detecting a
hybridization complex; wherein the presence of a hybridization
complex correlates with the presence of a splice variant nucleic
acid sequence in the biological sample.
According to the present invention, the splice variants described
herein are non-limiting examples of markers for diagnosing cardiac
disease and/or cardiac pathology, including but not limited to
cardiac damage. Each splice variant marker of the present invention
can be used alone or in combination, for various uses, including
but not limited to, prognosis, prediction, screening, early
diagnosis, determination of progression, therapy selection and
treatment monitoring of cardiac disease and/or cardiac pathology,
including but not limited to cardiac damage.
According to optional but preferred embodiments of the present
invention, any marker according to the present invention may
optionally be used alone or combination. Such a combination may
optionally comprise a plurality of markers described herein,
optionally including any subcombination of markers, and/or a
combination featuring at least one other marker, for example a
known marker. Furthermore, such a combination may optionally and
preferably be used as described above with regard to determining a
ratio between a quantitative or semi-quantitative measurement of
any marker described herein to any other marker described herein,
and/or any other known marker, and/or any other marker. With regard
to such a ratio between any marker described herein (or a
combination thereof) and a known marker, more preferably the known
marker comprises the "known protein" as described in greater detail
below with regard to each cluster or gene.
According to other preferred embodiments of the present invention,
a splice variant protein or a fragment thereof, or a splice variant
nucleic acid sequence or a fragment thereof, may be featured as a
biomarker for detecting cardiac disease and/or cardiac pathology,
including but not limited to cardiac damage, such that a biomarker
may optionally comprise any of the above. According to still other
preferred embodiments, the present invention optionally and
preferably encompasses any amino acid sequence or fragment thereof
encoded by a nucleic acid sequence corresponding to a splice
variant protein as described herein. Any oligopeptide or peptide
relating to such an amino acid sequence or fragment thereof may
optionally also (additionally or alternatively) be used as a
biomarker, including but not limited to the unique amino acid
sequences of these proteins that are depicted as tails, heads,
insertions, edges or bridges. The present invention also optionally
encompasses antibodies capable of recognizing, and/or being
elicited by, such oligopeptides or peptides.
The present invention also optionally and preferably encompasses
any nucleic acid sequence or fragment thereof, or amino acid
sequence or fragment thereof, corresponding to a splice variant of
the present invention as described above, optionally for any
application.
Non-limiting examples of methods or assays are described below.
The present invention also relates to kits based upon such
diagnostic methods or assays.
Nucleic Acid Sequences and Oligonucleotides
Various embodiments of the present invention encompass nucleic acid
sequences described hereinabove; fragments thereof, sequences
hybridizable therewith, sequences homologous thereto, sequences
encoding similar polypeptides with different codon usage, altered
sequences characterized by mutations, such as deletion, insertion
or substitution of one or more nucleotides, either naturally
occurring or artificially induced, either randomly or in a targeted
fashion.
The present invention encompasses nucleic acid sequences described
herein; fragments thereof, sequences hybridizable therewith,
sequences homologous thereto [e.g., at least 50%, at least 55%, at
least 60%, at least 65%, at least 70%, at least 75%, at least 80%,
at least 85%, at least 95% or more say 100% identical to the
nucleic acid sequences set forth below], sequences encoding similar
polypeptides with different codon usage, altered sequences
characterized by mutations, such as deletion, insertion or
substitution of one or more nucleotides, either naturally occurring
or man induced, either randomly or in a targeted fashion. The
present invention also encompasses homologous nucleic acid
sequences (i.e., which form a part of a polynucleotide sequence of
the present invention) which include sequence regions unique to the
polynucleotides of the present invention.
In cases where the polynucleotide sequences of the present
invention encode previously unidentified polypeptides, the present
invention also encompasses novel polypeptides or portions thereof,
which are encoded by the isolated polynucleotide and respective
nucleic acid fragments thereof described hereinabove.
A "nucleic acid fragment" or an "oligonucleotide" or a
"polynucleotide" are used herein interchangeably to refer to a
polymer of nucleic acids. A polynucleotide sequence of the present
invention refers to a single or double stranded nucleic acid
sequences which is isolated and provided in the form of an RNA
sequence, a complementary polynucleotide sequence (cDNA), a genomic
polynucleotide sequence and/or a composite polynucleotide sequences
(e.g., a combination of the above).
As used herein the phrase "complementary polynucleotide sequence"
refers to a sequence, which results from reverse transcription of
messenger RNA using a reverse transcriptase or any other RNA
dependent DNA polymerase. Such a sequence can be subsequently
amplified in vivo or in vitro using a DNA dependent DNA
polymerase.
As used herein the phrase "genomic polynucleotide sequence" refers
to a sequence derived (isolated) from a chromosome and thus it
represents a contiguous portion of a chromosome.
As used herein the phrase "composite polynucleotide sequence"
refers to a sequence, which is composed of genomic and cDNA
sequences. A composite sequence can include some exonal sequences
required to encode the polypeptide of the present invention, as
well as some intronic sequences interposing therebetween. The
intronic sequences can be of any source, including of other genes,
and typically will include conserved splicing signal sequences.
Such intronic sequences may further include cis acting expression
regulatory elements.
Preferred embodiments of the present invention encompass
oligonucleotide probes.
An example of an oligonucleotide probe which can be utilized by the
present invention is a single stranded polynucleotide which
includes a sequence complementary to the unique sequence region of
any variant according to the present invention, including but not
limited to a nucleotide sequence coding for an amino sequence of a
bridge, tail, head and/or insertion according to the present
invention, and/or the equivalent portions of any nucleotide
sequence given herein (including but not limited to a nucleotide
sequence of a node, segment or amplicon described herein).
Alternatively, an oligonucleotide probe of the present invention
can be designed to hybridize with a nucleic acid sequence
encompassed by any of the above nucleic acid sequences,
particularly the portions specified above, including but not
limited to a nucleotide sequence coding for an amino sequence of a
bridge, tail, head and/or insertion according to the present
invention, and/or the equivalent portions of any nucleotide
sequence given herein (including but not limited to a nucleotide
sequence of a node, segment or amplicon described herein).
Oligonucleotides designed according to the teachings of the present
invention can be generated according to any oligonucleotide
synthesis method known in the art such as enzymatic synthesis or
solid phase synthesis. Equipment and reagents for executing
solid-phase synthesis are commercially available from, for example,
Applied Biosystems. Any other means for such synthesis may also be
employed; the actual synthesis of the oligonucleotides is well
within the capabilities of one skilled in the art and can be
accomplished via established methodologies as detailed in, for
example, "Molecular Cloning: A laboratory Manual" Sambrook et al.,
(1989); "Current Protocols in Molecular Biology" Volumes I-III
Ausubel, R. M., ed. (1994); Ausubel et al., "Current Protocols in
Molecular Biology", John Wiley and Sons, Baltimore, Md. (1989);
Perbal, "A Practical Guide to Molecular Cloning", John Wiley &
Sons, New York (1988) and "Oligonucleotide Synthesis" Gait, M. J.,
ed. (1984) utilizing solid phase chemistry, e.g. cyanoethyl
phosphoramidite followed by deprotection, desalting and
purification by for example, an automated trityl-on method or
HPLC.
Oligonucleotides used according to this aspect of the present
invention are those having a length selected from a range of about
10 to about 200 bases preferably about 15 to about 150 bases, more
preferably about 20 to about 100 bases, most preferably about 20 to
about 50 bases. Preferably, the oligonucleotide of the present
invention features at least 17, at least 18, at least 19, at least
20, at least 22, at least 25, at least 30 or at least 40, bases
specifically hybridizable with the biomarkers of the present
invention.
The oligonucleotides of the present invention may comprise
heterocylic nucleosides consisting of purines and the pyrimidines
bases, bonded in a 3' to 5' phosphodiester linkage.
Preferably used oligonucleotides are those modified at one or more
of the backbone, internucleoside linkages or bases, as is broadly
described hereinunder.
Specific examples of preferred oligonucleotides useful according to
this aspect of the present invention include oligonucleotides
containing modified backbones or non-natural internucleoside
linkages. Oligonucleotides having modified backbones include those
that retain a phosphorus atom in the backbone, as disclosed in U.S.
Pat. Nos. 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897;
5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676;
5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126;
5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361;
and 5,625,050.
Preferred modified oligonucleotide backbones include, for example,
phosphorothioates, chiral phosphorothioates, phosphorodithioates,
phosphotriesters, aminoalkyl phosphotriesters, methyl and other
alkyl phosphonates including 3'-alkylene phosphonates and chiral
phosphonates, phosphinates, phosphoramidates including 3'-amino
phosphoramidate and aminoalkylphosphoramidates,
thionophosphoramidates, thionoalkylphosphonates,
thionoalkylphosphotriesters, and boranophosphates having normal
3'-5' linkages, 2'-5' linked analogs of these, and those having
inverted polarity wherein the adjacent pairs of nucleoside units
are linked 3'-5' to 5'-3' or 2'-5' to 5'-2'. Various salts, mixed
salts and free acid forms can also be used.
Alternatively, modified oligonucleotide backbones that do not
include a phosphorus atom therein have backbones that are formed by
short chain alkyl or cycloalkyl internucleoside linkages, mixed
heteroatom and alkyl or cycloalkyl internucleoside linkages, or one
or more short chain heteroatomic or heterocyclic internucleoside
linkages. These include those having morpholino linkages (formed in
part from the sugar portion of a nucleoside); siloxane backbones;
sulfide, sulfoxide and sulfone backbones; formacetyl and
thioformacetyl backbones; methylene formacetyl and thioformacetyl
backbones; alkene containing backbones; sulfamate backbones;
methyleneimino and methylenehydrazino backbones; sulfonate and
sulfonamide backbones; amide backbones; and others having mixed N,
O, S and CH.sub.2 component parts, as disclosed in U.S. Pat. Nos.
5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033;
5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967;
5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289;
5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312;
5,633,360; 5,677,437; and 5,677,439.
Other oligonucleotides which can be used according to the present
invention, are those modified in both sugar and the internucleoside
linkage, i.e., the backbone, of the nucleotide units are replaced
with novel groups. The base units are maintained for
complementation with the appropriate polynucleotide target. An
example for such an oligonucleotide mimetic, includes peptide
nucleic acid (PNA). United States patents that teach the
preparation of PNA compounds include, but are not limited to, U.S.
Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is
herein incorporated by reference. Other backbone modifications,
which can be used in the present invention are disclosed in U.S.
Pat. No. 6,303,374.
Oligonucleotides of the present invention may also include base
modifications or substitutions. As used herein, "unmodified" or
"natural" bases include the purine bases adenine (A) and guanine
(G), and the pyrimidine bases thymine (T), cytosine (C) and uracil
(U). Modified bases include but are not limited to other synthetic
and natural bases such as 5-methylcytosine (5-me-C),
5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine,
6-methyl and other alkyl derivatives of adenine and guanine,
2-propyl and other alkyl derivatives of adenine and guanine,
2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and
cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine
and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo,
8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted
adenines and guanines, 5-halo particularly 5-bromo,
5-trifluoromethyl and other 5-substituted uracils and cytosines,
7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine,
7-deazaguanine and 7-deazaadenine and 3-deazaguanine and
3-deazaadenine. Further bases particularly useful for increasing
the binding affinity of the oligomeric compounds of the invention
include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6
and O-6 substituted purines, including 2-aminopropyladenine,
5-propynyluracil and 5-propynylcytosine. 5-methylcytosine
substitutions have been shown to increase nucleic acid duplex
stability by 0.6-1.2.degree. C. and are presently preferred base
substitutions, even more particularly when combined with
2'-O-methoxyethyl sugar modifications.
Another modification of the oligonucleotides of the invention
involves chemically linking to the oligonucleotide one or more
moieties or conjugates, which enhance the activity, cellular
distribution or cellular uptake of the oligonucleotide. Such
moieties include but are not limited to lipid moieties such as a
cholesterol moiety, cholic acid, a thioether, e.g.,
hexyl-S-tritylthiol, a thiocholesterol, an aliphatic chain, e.g.,
dodecandiol or undecyl residues, a phospholipid, e.g.,
di-hexadecyl-rac-glycerol or triethylammonium
1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or a
polyethylene glycol chain, or adamantane acetic acid, a palmityl
moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol
moiety, as disclosed in U.S. Pat. No. 6,303,374.
It is not necessary for all positions in a given oligonucleotide
molecule to be uniformly modified, and in fact more than one of the
aforementioned modifications may be incorporated in a single
compound or even at a single nucleoside within an
oligonucleotide.
It will be appreciated that oligonucleotides of the present
invention may include further modifications for more efficient use
as diagnostic agents and/or to increase bioavailability,
therapeutic efficacy and reduce cytotoxicity.
To enable cellular expression of the polynucleotides of the present
invention, a nucleic acid construct according to the present
invention may be used, which includes at least a coding region of
one of the above nucleic acid sequences, and further includes at
least one cis acting regulatory element. As used herein, the phrase
"cis acting regulatory element" refers to a polynucleotide
sequence, preferably a promoter, which binds a trans acting
regulator and regulates the transcription of a coding sequence
located downstream thereto.
Any suitable promoter sequence can be used by the nucleic acid
construct of the present invention.
Preferably, the promoter utilized by the nucleic acid construct of
the present invention is active in the specific cell population
transformed. Examples of cell type-specific and/or tissue-specific
promoters include promoters such as albumin that is liver specific,
lymphoid specific promoters [Calame et al., (1988) Adv. Immunol.
43:235-275]; in particular promoters of T-cell receptors [Winoto et
al., (1989) EMBO J. 8:729-733] and immunoglobulins; [Banerji et al.
(1983) Cell 33729-740], neuron-specific promoters such as the
neurofilament promoter [Byrne et al. (1989) Proc. Natl. Acad. Sci.
USA 86:5473-5477], pancreas-specific promoters [Edlunch et al.
(1985) Science 230:912-916] or mammary gland-specific promoters
such as the milk whey promoter (U.S. Pat. No. 4,873,316 and
European Application Publication No. 264,166). The nucleic acid
construct of the present invention can further include an enhancer,
which can be adjacent or distant to the promoter sequence and can
function in up regulating the transcription therefrom.
The nucleic acid construct of the present invention preferably
further includes an appropriate selectable marker and/or an origin
of replication. Preferably, the nucleic acid construct utilized is
a shuttle vector, which can propagate both in E. coli (wherein the
construct comprises an appropriate selectable marker and origin of
replication) and be compatible for propagation in cells, or
integration in a gene and a tissue of choice. The construct
according to the present invention can be, for example, a plasmid,
a bacmid, a phagemid, a cosmid, a phage, a virus or an artificial
chromosome.
Examples of suitable constructs include, but are not limited to,
pcDNA3, pcDNA3.1 (+/-), pGL3, PzeoSV2 (+/-), pDisplay,
pEF/myc/cyto, pCMV/myc/cyto each of which is commercially available
from Invitrogen Co. (dot invitrogen dot com). Examples of
retroviral vector and packaging systems are those sold by Clontech,
San Diego, Calif., including Retro-X vectors pLNCX and pLXSN, which
permit cloning into multiple cloning sites and the trasgene is
transcribed from CMV promoter. Vectors derived from Mo-MuLV are
also included such as pBabe, where the transgene will be
transcribed from the 5'LTR promoter.
Currently preferred in vivo nucleic acid transfer techniques
include transfection with viral or non-viral constructs, such as
adenovirus, lentivirus, Herpes simplex I virus, or adeno-associated
virus (AAV) and lipid-based systems. Useful lipids for
lipid-mediated transfer of the gene are, for example, DOTMA, DOPE,
and DC-Chol [Tonkinson et al., Cancer Investigation, 14(1): 54-65
(1996)]. The most preferred constructs for use in gene therapy are
viruses, most preferably adenoviruses, AAV, lentiviruses, or
retroviruses. A viral construct such as a retroviral construct
includes at least one transcriptional promoter/enhancer or
locus-defining element(s), or other elements that control gene
expression by other means such as alternate splicing, nuclear RNA
export, or post-translational modification of messenger. Such
vector constructs also include a packaging signal, long terminal
repeats (LTRs) or portions thereof, and positive and negative
strand primer binding sites appropriate to the virus used, unless
it is already present in the viral construct. In addition, such a
construct typically includes a signal sequence for secretion of the
peptide from a host cell in which it is placed. Preferably the
signal sequence for this purpose is a mammalian signal sequence or
the signal sequence of the polypeptide variants of the present
invention. Optionally, the construct may also include a signal that
directs polyadenylation, as well as one or more restriction sites
and a translation termination sequence. By way of example, such
constructs will typically include a 5' LTR, a tRNA binding site, a
packaging signal, an origin of second-strand DNA synthesis, and a
3' LTR or a portion thereof. Other vectors can be used that are
non-viral, such as cationic lipids, polylysine, and dendrimers.
Hybridization Assays
Detection of a nucleic acid of interest in a biological sample may
optionally be effected by hybridization-based assays using an
oligonucleotide probe (non-limiting examples of probes according to
the present invention were previously described).
Traditional hybridization assays include PCR, RT-PCR, Real-time
PCR, RNase protection, in-situ hybridization, primer extension,
Southern blots (DNA detection), dot or slot blots (DNA, RNA), and
Northern blots (RNA detection) (NAT type assays are described in
greater detail below). More recently, PNAs have been described
(Nielsen et al. 1999, Current Opin. Biotechnol. 10:71-75). Other
detection methods include kits containing probes on a dipstick
setup and the like.
Hybridization based assays which allow the detection of a variant
of interest (i.e., DNA or RNA) in a biological sample rely on the
use of oligonucleotides which can be 10, 15, 20, or 30 to 100
nucleotides long preferably from 10 to 50, more preferably from 40
to 50 nucleotides long.
Thus, the isolated polynucleotides (oligonucleotides) of the
present invention are preferably hybridizable with any of the
herein described nucleic acid sequences under moderate to stringent
hybridization conditions.
Moderate to stringent hybridization conditions are characterized by
a hybridization solution such as containing 10% dextrane sulfate, 1
M NaCl, 1% SDS and 5.times.10.sup.6 cpm .sup.32P labeled probe, at
65.degree. C., with a final wash solution of 0.2.times.SSC and 0.1%
SDS and final wash at 65.degree. C. and whereas moderate
hybridization is effected using a hybridization solution containing
10% dextrane sulfate, 1 M NaCl, 1% SDS and 5.times.10.sup.6 cpm
.sup.32P labeled probe, at 65.degree. C., with a final wash
solution of 1.times.SSC and 0.1% SDS and final wash at 50.degree.
C.
More generally, hybridization of short nucleic acids (below 200 bp
in length, e.g. 17-40 bp in length) can be effected using the
following exemplary hybridization protocols which can be modified
according to the desired stringency; (i) hybridization solution of
6.times.SSC and 1% SDS or 3 M TMACI, 0.01 M sodium phosphate (pH
6.8), 1 mM EDTA (pH 7.6), 0.5% SDS, 100 .mu.g/ml denatured salmon
sperm DNA and 0.1% nonfat dried milk, hybridization temperature of
1-1.5.degree. C. below the T.sub.m, final wash solution of 3 M
TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5%
SDS at 1-1.5.degree. C. below the T.sub.m; (ii) hybridization
solution of 6.times.SSC and 0.1% SDS or 3 M TMACI, 0.01 M sodium
phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS, 100 .mu.g/ml
denatured salmon sperm DNA and 0.1% nonfat dried milk,
hybridization temperature of 2-2.5.degree. C. below the T.sub.m,
final wash solution of 3 M TMACI, 0.01 M sodium phosphate (pH 6.8),
1 mM EDTA (pH 7.6), 0.5% SDS at 1-1.5.degree. C. below the T.sub.m,
final wash solution of 6.times.SSC, and final wash at 22.degree.
C.; (iii) hybridization solution of 6.times.SSC and 1% SDS or 3 M
TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5%
SDS, 100 .mu.g/ml denatured salmon sperm DNA and 0.1% nonfat dried
milk, hybridization temperature.
The detection of hybrid duplexes can be carried out by a number of
methods. Typically, hybridization duplexes are separated from
unhybridized nucleic acids and the labels bound to the duplexes are
then detected. Such labels refer to radioactive, fluorescent,
biological or enzymatic tags or labels of standard use in the art.
A label can be conjugated to either the oligonucleotide probes or
the nucleic acids derived from the biological sample.
Probes can be labeled according to numerous well known methods.
Non-limiting examples of radioactive labels include 3H, 14C, 32P,
and 35S. Non-limiting examples of detectable markers include
ligands, fluorophores, chemiluminescent agents, enzymes, and
antibodies. Other detectable markers for use with probes, which can
enable an increase in sensitivity of the method of the invention,
include biotin and radio-nucleotides. It will become evident to the
person of ordinary skill that the choice of a particular label
dictates the manner in which it is bound to the probe.
For example, oligonucleotides of the present invention can be
labeled subsequent to synthesis, by incorporating biotinylated
dNTPs or rNTP, or some similar means (e.g., photo-cross-linking a
psoralen derivative of biotin to RNAs), followed by addition of
labeled streptavidin (e.g., phycoerythrin-conjugated streptavidin)
or the equivalent. Alternatively, when fluorescently-labeled
oligonucleotide probes are used, fluorescein, lissamine,
phycoerythrin, rhodamine (Perkin Elmer Cetus), Cy2, Cy3, Cy3.5,
Cy5, Cy5.5, Cy7, Fluor X (Amersham) and others [e.g., Kricka et al.
(1992), Academic Press San Diego, Calif.] can be attached to the
oligonucleotides.
Those skilled in the art will appreciate that wash steps may be
employed to wash away excess target DNA or probe as well as unbound
conjugate. Further, standard heterogeneous assay formats are
suitable for detecting the hybrids using the labels present on the
oligonucleotide primers and probes.
It will be appreciated that a variety of controls may be usefully
employed to improve accuracy of hybridization assays. For instance,
samples may be hybridized to an irrelevant probe and treated with
RNAse A prior to hybridization, to assess false hybridization.
Although the present invention is not specifically dependent on the
use of a label for the detection of a particular nucleic acid
sequence, such a label might be beneficial, by increasing the
sensitivity of the detection. Furthermore, it enables automation.
Probes can be labeled according to numerous well known methods.
As commonly known, radioactive nucleotides can be incorporated into
probes of the invention by several methods. Non-limiting examples
of radioactive labels include .sup.3H, .sup.14C, .sup.32P, and
.sup.35S.
Those skilled in the art will appreciate that wash steps may be
employed to wash away excess target DNA or probe as well as unbound
conjugate. Further, standard heterogeneous assay formats are
suitable for detecting the hybrids using the labels present on the
oligonucleotide primers and probes.
It will be appreciated that a variety of controls may be usefully
employed to improve accuracy of hybridization assays.
Probes of the invention can be utilized with naturally occurring
sugar-phosphate backbones as well as modified backbones including
phosphorothioates, dithionates, alkyl phosphonates and
a-nucleotides and the like. Probes of the invention can be
constructed of either ribonucleic acid (RNA) or deoxyribonucleic
acid (DNA), and preferably of DNA.
NAT Assays
Detection of a nucleic acid of interest in a biological sample may
also optionally be effected by NAT-based assays, which involve
nucleic acid amplification technology, such as PCR for example (or
variations thereof such as real-time PCR for example).
As used herein, a "primer" defines an oligonucleotide which is
capable of annealing to (hybridizing with) a target sequence,
thereby creating a double stranded region which can serve as an
initiation point for DNA synthesis under suitable conditions.
Amplification of a selected, or target, nucleic acid sequence may
be carried out by a number of suitable methods. See generally Kwoh
et al., 1990, Am. Biotechnol. Lab. 8:14 Numerous amplification
techniques have been described and can be readily adapted to suit
particular needs of a person of ordinary skill. Non-limiting
examples of amplification techniques include polymerase chain
reaction (PCR), ligase chain reaction (LCR), strand displacement
amplification (SDA), transcription-based amplification, the q3
replicase system and NASBA (Kwoh et al., 1989, Proc. NatI. Acad.
Sci. USA 86, 1173-1177; Lizardi et al., 1988, BioTechnology
6:1197-1202; Malek et al., 1994, Methods Mol. Biol., 28:253-260;
and Sambrook et al., 1989, supra).
The terminology "amplification pair" (or "primer pair") refers
herein to a pair of oligonucleotides (oligos) of the present
invention, which are selected to be used together in amplifying a
selected nucleic acid sequence by one of a number of types of
amplification processes, preferably a polymerase chain reaction.
Other types of amplification processes include ligase chain
reaction, strand displacement amplification, or nucleic acid
sequence-based amplification, as explained in greater detail below.
As commonly known in the art, the oligos are designed to bind to a
complementary sequence under selected conditions.
In one particular embodiment, amplification of a nucleic acid
sample from a patient is amplified under conditions which favor the
amplification of the most abundant differentially expressed nucleic
acid. In one preferred embodiment, RT-PCR is carried out on an mRNA
sample from a patient under conditions which favor the
amplification of the most abundant mRNA. In another preferred
embodiment, the amplification of the differentially expressed
nucleic acids is carried out simultaneously. It will be realized by
a person skilled in the art that such methods could be adapted for
the detection of differentially expressed proteins instead of
differentially expressed nucleic acid sequences.
The nucleic acid (i.e. DNA or RNA) for practicing the present
invention may be obtained according to well known methods.
Oligonucleotide primers of the present invention may be of any
suitable length, depending on the particular assay format and the
particular needs and targeted genomes employed. Optionally, the
oligonucleotide primers are at least 12 nucleotides in length,
preferably between 15 and 24 molecules, and they may be adapted to
be especially suited to a chosen nucleic acid amplification system.
As commonly known in the art, the oligonucleotide primers can be
designed by taking into consideration the melting point of
hybridization thereof with its targeted sequence (Sambrook et al.,
1989, Molecular Cloning--A Laboratory Manual, 2nd Edition, CSH
Laboratories; Ausubel et al., 1989, in Current Protocols in
Molecular Biology, John Wiley & Sons Inc., N.Y.).
It will be appreciated that antisense oligonucleotides may be
employed to quantify expression of a splice isoform of interest.
Such detection is effected at the pre-mRNA level. Essentially the
ability to quantitate transcription from a splice site of interest
can be effected based on splice site accessibility.
Oligonucleotides may compete with splicing factors for the splice
site sequences. Thus, low activity of the antisense oligonucleotide
is indicative of splicing activity.
The polymerase chain reaction and other nucleic acid amplification
reactions are well known in the art (various non-limiting examples
of these reactions are described in greater detail below). The pair
of oligonucleotides according to this aspect of the present
invention are preferably selected to have compatible melting
temperatures (Tm), e.g., melting temperatures which differ by less
than that 7.degree. C., preferably less than 5.degree. C., more
preferably less than 4.degree. C., most preferably less than
3.degree. C., ideally between 3.degree. C. and 0.degree. C.
Polymerase Chain Reaction (PCR): The polymerase chain reaction
(PCR), as described in U.S. Pat. Nos. 4,683,195 and 4,683,202 to
Mullis and Mullis et al., is a method of increasing the
concentration of a segment of target sequence in a mixture of
genomic DNA without cloning or purification. This technology
provides one approach to the problems of low target sequence
concentration. PCR can be used to directly increase the
concentration of the target to an easily detectable level. This
process for amplifying the target sequence involves the
introduction of a molar excess of two oligonucleotide primers which
are complementary to their respective strands of the
double-stranded target sequence to the DNA mixture containing the
desired target sequence. The mixture is denatured and then allowed
to hybridize. Following hybridization, the primers are extended
with polymerase so as to form complementary strands. The steps of
denaturation, hybridization (annealing), and polymerase extension
(elongation) can be repeated as often as needed, in order to obtain
relatively high concentrations of a segment of the desired target
sequence.
The length of the segment of the desired target sequence is
determined by the relative positions of the primers with respect to
each other, and, therefore, this length is a controllable
parameter. Because the desired segments of the target sequence
become the dominant sequences (in terms of concentration) in the
mixture, they are said to be "PCR-amplified."
Ligase Chain Reaction (LCR or LAR): The ligase chain reaction [LCR;
sometimes referred to as "Ligase Amplification Reaction" (LAR)] has
developed into a well-recognized alternative method of amplifying
nucleic acids. In LCR, four oligonucleotides, two adjacent
oligonucleotides which uniquely hybridize to one strand of target
DNA, and a complementary set of adjacent oligonucleotides, which
hybridize to the opposite strand are mixed and DNA ligase is added
to the mixture. Provided that there is complete complementarity at
the junction, ligase will covalently link each set of hybridized
molecules. Importantly, in LCR, two probes are ligated together
only when they base-pair with sequences in the target sample,
without gaps or mismatches. Repeated cycles of denaturation, and
ligation amplify a short segment of DNA. LCR has also been used in
combination with PCR to achieve enhanced detection of single-base
changes: see for example Segev, PCT Publication No. W09001069 A1
(1990). However, because the four oligonucleotides used in this
assay can pair to form two short ligatable fragments, there is the
potential for the generation of target-independent background
signal. The use of LCR for mutant screening is limited to the
examination of specific nucleic acid positions.
Self-Sustained Synthetic Reaction (3SR/NASBA): The self-sustained
sequence replication reaction (3SR) is a transcription-based in
vitro amplification system that can exponentially amplify RNA
sequences at a uniform temperature. The amplified RNA can then be
utilized for mutation detection. In this method, an oligonucleotide
primer is used to add a phage RNA polymerase promoter to the 5' end
of the sequence of interest. In a cocktail of enzymes and
substrates that includes a second primer, reverse transcriptase,
RNase H, RNA polymerase and ribo- and deoxyribonucleoside
triphosphates, the target sequence undergoes repeated rounds of
transcription, cDNA synthesis and second-strand synthesis to
amplify the area of interest. The use of 3SR to detect mutations is
kinetically limited to screening small segments of DNA (e.g.,
200-300 base pairs).
Q-Beta (Q.beta.) Replicase: In this method, a probe which
recognizes the sequence of interest is attached to the replicatable
RNA template for Q.beta. replicase. A previously identified major
problem with false positives resulting from the replication of
unhybridized probes has been addressed through use of a
sequence-specific ligation step. However, available thermostable
DNA ligases are not effective on this RNA substrate, so the
ligation must be performed by T4 DNA ligase at low temperatures (37
degrees C.). This prevents the use of high temperature as a means
of achieving specificity as in the LCR, the ligation event can be
used to detect a mutation at the junction site, but not
elsewhere.
A successful diagnostic method must be very specific. A
straight-forward method of controlling the specificity of nucleic
acid hybridization is by controlling the temperature of the
reaction. While the 3SR/NASBA, and Q.beta. systems are all able to
generate a large quantity of signal, one or more of the enzymes
involved in each cannot be used at high temperature (i.e., >55
degrees C.). Therefore the reaction temperatures cannot be raised
to prevent non-specific hybridization of the probes. If probes are
shortened in order to make them melt more easily at low
temperatures, the likelihood of having more than one perfect match
in a complex genome increases. For these reasons, PCR and LCR
currently dominate the research field in detection
technologies.
The basis of the amplification procedure in the PCR and LCR is the
fact that the products of one cycle become usable templates in all
subsequent cycles, consequently doubling the population with each
cycle. The final yield of any such doubling system can be expressed
as: (1+X).sup.n=y, where "X" is the mean efficiency (percent copied
in each cycle), "n" is the number of cycles, and "y" is the overall
efficiency, or yield of the reaction. If every copy of a target DNA
is utilized as a template in every cycle of a polymerase chain
reaction, then the mean efficiency is 100%. If 20 cycles of PCR are
performed, then the yield will be 2.sup.20, or 1,048,576 copies of
the starting material. If the reaction conditions reduce the mean
efficiency to 85%, then the yield in those 20 cycles will be only
1.85.sup.20, or 220,513 copies of the starting material. In other
words, a PCR running at 85% efficiency will yield only 21% as much
final product, compared to a reaction running at 100% efficiency. A
reaction that is reduced to 50% mean efficiency will yield less
than 1% of the possible product.
In practice, routine polymerase chain reactions rarely achieve the
theoretical maximum yield, and PCRs are usually run for more than
20 cycles to compensate for the lower yield. At 50% mean
efficiency, it would take 34 cycles to achieve the million-fold
amplification theoretically possible in 20, and at lower
efficiencies, the number of cycles required becomes prohibitive. In
addition, any background products that amplify with a better mean
efficiency than the intended target will become the dominant
products.
Also, many variables can influence the mean efficiency of PCR,
including target DNA length and secondary structure, primer length
and design, primer and dNTP concentrations, and buffer composition,
to name but a few. Contamination of the reaction with exogenous DNA
(e.g., DNA spilled onto lab surfaces) or cross-contamination is
also a major consideration. Reaction conditions must be carefully
optimized for each different primer pair and target sequence, and
the process can take days, even for an experienced investigator.
The laboriousness of this process, including numerous technical
considerations and other factors, presents a significant drawback
to using PCR in the clinical setting. Indeed, PCR has yet to
penetrate the clinical market in a significant way. The same
concerns arise with LCR, as LCR must also be optimized to use
different oligonucleotide sequences for each target sequence. In
addition, both methods require expensive equipment, capable of
precise temperature cycling.
Many applications of nucleic acid detection technologies, such as
in studies of allelic variation, involve not only detection of a
specific sequence in a complex background, but also the
discrimination between sequences with few, or single, nucleotide
differences. One method of the detection of allele-specific
variants by PCR is based upon the fact that it is difficult for Taq
polymerase to synthesize a DNA strand when there is a mismatch
between the template strand and the 3' end of the primer. An
allele-specific variant may be detected by the use of a primer that
is perfectly matched with only one of the possible alleles; the
mismatch to the other allele acts to prevent the extension of the
primer, thereby preventing the amplification of that sequence. This
method has a substantial limitation in that the base composition of
the mismatch influences the ability to prevent extension across the
mismatch, and certain mismatches do not prevent extension or have
only a minimal effect.
A similar 3'-mismatch strategy is used with greater effect to
prevent ligation in the LCR. Any mismatch effectively blocks the
action of the thermostable ligase, but LCR still has the drawback
of target-independent background ligation products initiating the
amplification. Moreover, the combination of PCR with subsequent LCR
to identify the nucleotides at individual positions is also a
clearly cumbersome proposition for the clinical laboratory.
The direct detection method according to various preferred
embodiments of the present invention may be, for example a cycling
probe reaction (CPR) or a branched DNA analysis.
When a sufficient amount of a nucleic acid to be detected is
available, there are advantages to detecting that sequence
directly, instead of making more copies of that target, (e.g., as
in PCR and LCR). Most notably, a method that does not amplify the
signal exponentially is more amenable to quantitative analysis.
Even if the signal is enhanced by attaching multiple dyes to a
single oligonucleotide, the correlation between the final signal
intensity and amount of target is direct. Such a system has an
additional advantage that the products of the reaction will not
themselves promote further reaction, so contamination of lab
surfaces by the products is not as much of a concern. Recently
devised techniques have sought to eliminate the use of
radioactivity and/or improve the sensitivity in automatable
formats. Two examples are the "Cycling Probe Reaction" (CPR), and
"Branched DNA" (bDNA).
Cycling probe reaction (CPR): The cycling probe reaction (CPR),
uses a long chimeric oligonucleotide in which a central portion is
made of RNA while the two termini are made of DNA. Hybridization of
the probe to a target DNA and exposure to a thermostable RNase H
causes the RNA portion to be digested. This destabilizes the
remaining DNA portions of the duplex, releasing the remainder of
the probe from the target DNA and allowing another probe molecule
to repeat the process. The signal, in the form of cleaved probe
molecules, accumulates at a linear rate. While the repeating
process increases the signal, the RNA portion of the
oligonucleotide is vulnerable to RNases that may carried through
sample preparation.
Branched DNA: Branched DNA (bDNA), involves oligonucleotides with
branched structures that allow each individual oligonucleotide to
carry 35 to 40 labels (e.g., alkaline phosphatase enzymes). While
this enhances the signal from a hybridization event, signal from
non-specific binding is similarly increased.
The detection of at least one sequence change according to various
preferred embodiments of the present invention may be accomplished
by, for example restriction fragment length polymorphism (RFLP
analysis), allele specific oligonucleotide (ASO) analysis,
Denaturing/Temperature Gradient Gel Electrophoresis (DGGE/TGGE),
Single-Strand Conformation Polymorphism (SSCP) analysis or Dideoxy
fingerprinting (ddF).
The demand for tests which allow the detection of specific nucleic
acid sequences and sequence changes is growing rapidly in clinical
diagnostics. As nucleic acid sequence data for genes from humans
and pathogenic organisms accumulates, the demand for fast,
cost-effective, and easy-to-use tests for as yet mutations within
specific sequences is rapidly increasing.
A handful of methods have been devised to scan nucleic acid
segments for mutations. One option is to determine the entire gene
sequence of each test sample (e.g., a bacterial isolate). For
sequences under approximately 600 nucleotides, this may be
accomplished using amplified material (e.g., PCR reaction
products). This avoids the time and expense associated with cloning
the segment of interest. However, specialized equipment and highly
trained personnel are required, and the method is too labor-intense
and expensive to be practical and effective in the clinical
setting.
In view of the difficulties associated with sequencing, a given
segment of nucleic acid may be characterized on several other
levels. At the lowest resolution, the size of the molecule can be
determined by electrophoresis by comparison to a known standard run
on the same gel. A more detailed picture of the molecule may be
achieved by cleavage with combinations of restriction enzymes prior
to electrophoresis, to allow construction of an ordered map. The
presence of specific sequences within the fragment can be detected
by hybridization of a labeled probe, or the precise nucleotide
sequence can be determined by partial chemical degradation or by
primer extension in the presence of chain-terminating nucleotide
analogs.
Restriction fragment length polymorphism (RFLP): For detection of
single-base differences between like sequences, the requirements of
the analysis are often at the highest level of resolution. For
cases in which the position of the nucleotide in question is known
in advance, several methods have been developed for examining
single base changes without direct sequencing. For example, if a
mutation of interest happens to fall within a restriction
recognition sequence, a change in the pattern of digestion can be
used as a diagnostic tool (e.g., restriction fragment length
polymorphism [RFLP] analysis).
Single point mutations have been also detected by the creation or
destruction of RFLPs. Mutations are detected and localized by the
presence and size of the RNA fragments generated by cleavage at the
mismatches. Single nucleotide mismatches in DNA heteroduplexes are
also recognized and cleaved by some chemicals, providing an
alternative strategy to detect single base substitutions,
generically named the "Mismatch Chemical Cleavage" (MCC). However,
this method requires the use of osmium tetroxide and piperidine,
two highly noxious chemicals which are not suited for use in a
clinical laboratory.
RFLP analysis suffers from low sensitivity and requires a large
amount of sample. When RFLP analysis is used for the detection of
point mutations, it is, by its nature, limited to the detection of
only those single base changes which fall within a restriction
sequence of a known restriction endonuclease. Moreover, the
majority of the available enzymes have 4 to 6 base-pair recognition
sequences, and cleave too frequently for many large-scale DNA
manipulations. Thus, it is applicable only in a small fraction of
cases, as most mutations do not fall within such sites.
A handful of rare-cutting restriction enzymes with 8 base-pair
specificities have been isolated and these are widely used in
genetic mapping, but these enzymes are few in number, are limited
to the recognition of G+C-rich sequences, and cleave at sites that
tend to be highly clustered. Recently, endonucleases encoded by
group I introns have been discovered that might have greater than
12 base-pair specificity, but again, these are few in number.
Allele specific oligonucleotide (ASO): If the change is not in a
recognition sequence, then allele-specific oligonucleotides (ASOs),
can be designed to hybridize in proximity to the mutated
nucleotide, such that a primer extension or ligation event can
bused as the indicator of a match or a mis-match. Hybridization
with radioactively labeled allelic specific oligonucleotides (ASO)
also has been applied to the detection of specific point mutations.
The method is based on the differences in the melting temperature
of short DNA fragments differing by a single nucleotide. Stringent
hybridization and washing conditions can differentiate between
mutant and wild-type alleles. The ASO approach applied to PCR
products also has been extensively utilized by various researchers
to detect and characterize point mutations in ras genes and gsp/gip
oncogenes. Because of the presence of various nucleotide changes in
multiple positions, the ASO method requires the use of many
oligonucleotides to cover all possible oncogenic mutations.
With either of the techniques described above (i.e., RFLP and ASO),
the precise location of the suspected mutation must be known in
advance of the test. That is to say, they are inapplicable when one
needs to detect the presence of a mutation within a gene or
sequence of interest.
Denaturing/Temperature Gradient Gel Electrophoresis (DGGE/TGGE):
Two other methods rely on detecting changes in electrophoretic
mobility in response to minor sequence changes. One of these
methods, termed "Denaturing Gradient Gel Electrophoresis" (DGGE) is
based on the observation that slightly different sequences will
display different patterns of local melting when
electrophoretically resolved on a gradient gel. In this manner,
variants can be distinguished, as differences in melting properties
of homoduplexes versus heteroduplexes differing in a single
nucleotide can detect the presence of mutations in the target
sequences because of the corresponding changes in their
electrophoretic mobilities. The fragments to be analyzed, usually
PCR products, are "clamped" at one end by a long stretch of G-C
base pairs (30-80) to allow complete denaturation of the sequence
of interest without complete dissociation of the strands. The
attachment of a GC "clamp" to the DNA fragments increases the
fraction of mutations that can be recognized by DGGE. Attaching a
GC clamp to one primer is critical to ensure that the amplified
sequence has a low dissociation temperature. Modifications of the
technique have been developed, using temperature gradients, and the
method can be also applied to RNA:RNA duplexes.
Limitations on the utility of DGGE include the requirement that the
denaturing conditions must be optimized for each type of DNA to be
tested. Furthermore, the method requires specialized equipment to
prepare the gels and maintain the needed high temperatures during
electrophoresis. The expense associated with the synthesis of the
clamping tail on one oligonucleotide for each sequence to be tested
is also a major consideration. In addition, long running times are
required for DGGE. The long running time of DGGE was shortened in a
modification of DGGE called constant denaturant gel electrophoresis
(CDGE). CDGE requires that gels be performed under different
denaturant conditions in order to reach high efficiency for the
detection of mutations.
A technique analogous to DGGE, termed temperature gradient gel
electrophoresis (TGGE), uses a thermal gradient rather than a
chemical denaturant gradient. TGGE requires the use of specialized
equipment which can generate a temperature gradient perpendicularly
oriented relative to the electrical field. TGGE can detect
mutations in relatively small fragments of DNA therefore scanning
of large gene segments requires the use of multiple PCR products
prior to running the gel.
Single-Strand Conformation Polymorphism (SSCP): Another common
method, called "Single-Strand Conformation Polymorphism" (SSCP) was
developed by Hayashi, Sekya and colleagues and is based on the
observation that single strands of nucleic acid can take on
characteristic conformations in non-denaturing conditions, and
these conformations influence electrophoretic mobility. The
complementary strands assume sufficiently different structures that
one strand may be resolved from the other. Changes in sequences
within the fragment will also change the conformation, consequently
altering the mobility and allowing this to be used as an assay for
sequence variations.
The SSCP process involves denaturing a DNA segment (e.g., a PCR
product) that is labeled on both strands, followed by slow
electrophoretic separation on a non-denaturing polyacrylamide gel,
so that intra-molecular interactions can form and not be disturbed
during the run. This technique is extremely sensitive to variations
in gel composition and temperature. A serious limitation of this
method is the relative difficulty encountered in comparing data
generated in different laboratories, under apparently similar
conditions.
Dideoxy fingerprinting (ddF): The dideoxy fingerprinting (ddF) is
another technique developed to scan genes for the presence of
mutations. The ddF technique combines components of Sanger dideoxy
sequencing with SSCP. A dideoxy sequencing reaction is performed
using one dideoxy terminator and then the reaction products are
electrophoresed on nondenaturing polyacrylamide gels to detect
alterations in mobility of the termination segments as in SSCP
analysis. While ddF is an improvement over SSCP in terms of
increased sensitivity, ddF requires the use of expensive
dideoxynucleotides and this technique is still limited to the
analysis of fragments of the size suitable for SSCP (i.e.,
fragments of 200-300 bases for optimal detection of mutations).
In addition to the above limitations, all of these methods are
limited as to the size of the nucleic acid fragment that can be
analyzed. For the direct sequencing approach, sequences of greater
than 600 base pairs require cloning, with the consequent delays and
expense of either deletion sub-cloning or primer walking, in order
to cover the entire fragment. SSCP and DGGE have even more severe
size limitations. Because of reduced sensitivity to sequence
changes, these methods are not considered suitable for larger
fragments. Although SSCP is reportedly able to detect 90% of
single-base substitutions within a 200 base-pair fragment, the
detection drops to less than 50% for 400 base pair fragments.
Similarly, the sensitivity of DGGE decreases as the length of the
fragment reaches 500 base-pairs. The ddF technique, as a
combination of direct sequencing and SSCP, is also limited by the
relatively small size of the DNA that can be screened.
According to a presently preferred embodiment of the present
invention the step of searching for any of the nucleic acid
sequences described here, in tumor cells or in cells derived from a
cancer patient is effected by any suitable technique, including,
but not limited to, nucleic acid sequencing, polymerase chain
reaction, ligase chain reaction, self-sustained synthetic reaction,
Q.beta.-Replicase, cycling probe reaction, branched DNA,
restriction fragment length polymorphism analysis, mismatch
chemical cleavage, heteroduplex analysis, allele-specific
oligonucleotides, denaturing gradient gel electrophoresis, constant
denaturant gel electrophoresis, temperature gradient gel
electrophoresis and dideoxy fingerprinting.
Detection may also optionally be performed with a chip or other
such device. The nucleic acid sample which includes the candidate
region to be analyzed is preferably isolated, amplified and labeled
with a reporter group. This reporter group can be a fluorescent
group such as phycoerythrin. The labeled nucleic acid is then
incubated with the probes immobilized on the chip using a fluidics
station. describe the fabrication of fluidics devices and
particularly microcapillary devices, in silicon and glass
substrates.
Once the reaction is completed, the chip is inserted into a scanner
and patterns of hybridization are detected. The hybridization data
is collected, as a signal emitted from the reporter groups already
incorporated into the nucleic acid, which is now bound to the
probes attached to the chip. Since the sequence and position of
each probe immobilized on the chip is known, the identity of the
nucleic acid hybridized to a given probe can be determined.
It will be appreciated that when utilized along with automated
equipment, the above described detection methods can be used to
screen multiple samples for a disease and/or pathological condition
both rapidly and easily.
Amino Acid Sequences and Peptides
The terms "polypeptide," "peptide" and "protein" are used
interchangeably herein to refer to a polymer of amino acid
residues. The terms apply to amino acid polymers in which one or
more amino acid residue is an analog or mimetic of a corresponding
naturally occurring amino acid, as well as to naturally occurring
amino acid polymers. Polypeptides can be modified, e.g., by the
addition of carbohydrate residues to form glycoproteins. The terms
"polypeptide," "peptide" and "protein" include glycoproteins, as
well as non-glycoproteins.
Polypeptide products can be biochemically synthesized such as by
employing standard solid phase techniques. Such methods include but
are not limited to exclusive solid phase synthesis, partial solid
phase synthesis methods, fragment condensation, classical solution
synthesis. These methods are preferably used when the peptide is
relatively short (i.e., 10 kDa) and/or when it cannot be produced
by recombinant techniques (i.e., not encoded by a nucleic acid
sequence) and therefore involves different chemistry.
Solid phase polypeptide synthesis procedures are well known in the
art and further described by John Morrow Stewart and Janis Dillaha
Young, Solid Phase Peptide Syntheses (2nd Ed., Pierce Chemical
Company, 1984).
Synthetic polypeptides can optionally be purified by preparative
high performance liquid chromatography [Creighton T. (1983)
Proteins, structures and molecular principles. WH Freeman and Co.
N.Y.], after which their composition can be confirmed via amino
acid sequencing.
In cases where large amounts of a polypeptide are desired, it can
be generated using recombinant techniques such as described by
Bitter et al., (1987) Methods in Enzymol. 153:516-544, Studier et
al. (1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984)
Nature 310:511-514, Takamatsu et al. (1987) EMBO J. 6:307-311,
Coruzzi et al. (1984) EMBO J. 3:1671-1680 and Brogli et al., (1984)
Science 224:838-843, Gurley et al. (1986) Mol. Cell. Biol.
6:559-565 and Weissbach & Weissbach, 1988, Methods for Plant
Molecular Biology, Academic Press, NY, Section VIII, pp
421-463.
The present invention also encompasses polypeptides encoded by the
polynucleotide sequences of the present invention, as well as
polypeptides according to the amino acid sequences described
herein. The present invention also encompasses homologues of these
polypeptides, such homologues can be at least 50%, at least 55%, at
least 60%, at least 65%, at least 70%, at least 75%, at least 80%,
at least 85%, at least 95% or more say 100% homologous to the amino
acid sequences set forth below, as can be determined using BlastP
software of the National Center of Biotechnology Information (NCBI)
using default parameters, optionally and preferably including the
following: filtering on (this option filters repetitive or
low-complexity sequences from the query using the Seg (protein)
program), scoring matrix is BLOSUM62 for proteins, word size is 3,
E value is 10, gap costs are 11, 1 (initialization and extension),
and number of alignments shown is 50. Optionally and preferably,
nucleic acid sequence homology (identity) is determined using
BlastN software of the National Center of Biotechnology Information
(NCBI) using default parameters, which preferably include using the
DUST filter program, and also preferably include having an E value
of 10, filtering low complexity sequences and a word size of 11.
Finally, the present invention also encompasses fragments of the
above described polypeptides and polypeptides having mutations,
such as deletions, insertions or substitutions of one or more amino
acids, either naturally occurring or artificially induced, either
randomly or in a targeted fashion.
It will be appreciated that peptides identified according the
present invention may be degradation products, synthetic peptides
or recombinant peptides as well as peptidomimetics, typically,
synthetic peptides and peptoids and semipeptoids which are peptide
analogs, which may have, for example, modifications rendering the
peptides more stable while in a body or more capable of penetrating
into cells. Such modifications include, but are not limited to N
terminus modification, C terminus modification, peptide bond
modification, including, but not limited to, CH2-NH, CH2-S,
CH2-S.dbd.O, O.dbd.C--NH, CH2-O, CH2-CH2, S.dbd.C--NH, CH.dbd.CH or
CF.dbd.CH, backbone modifications, and residue modification.
Methods for preparing peptidomimetic compounds are well known in
the art and are specified. Further details in this respect are
provided hereinunder.
Peptide bonds (--CO--NH--) within the peptide may be substituted,
for example, by N-methylated bonds (--N(CH3)-CO--), ester bonds
(--C(R)H--C--O--O--C(R)--N--), ketomethylen bonds (--CO--CH2-),
.alpha.-aza bonds (--NH--N(R)--CO--), wherein R is any alkyl, e.g.,
methyl, carba bonds (--CH2-NH--), hydroxyethylene bonds
(--CH(OH)--CH2-), thioamide bonds (--CS--NH--), olefinic double
bonds (--CH.dbd.CH--), retro amide bonds (--NH--CO--), peptide
derivatives (--N(R)--CH2-CO--), wherein R is the "normal" side
chain, naturally presented on the carbon atom.
These modifications can occur at any of the bonds along the peptide
chain and even at several (2-3) at the same time.
Natural aromatic amino acids, Trp, Tyr and Phe, may be substituted
for synthetic non-natural acid such as Phenylglycine, TIC,
naphthylelanine (Nol), ring-methylated derivatives of Phe,
halogenated derivatives of Phe or o-methyl-Tyr.
In addition to the above, the peptides of the present invention may
also include one or more modified amino acids or one or more
non-amino acid monomers (e.g. fatty acids, complex carbohydrates
etc).
As used herein in the specification and in the claims section below
the term "amino acid" or "amino acids" is understood to include the
20 naturally occurring amino acids; those amino acids often
modified post-translationally in vivo, including, for example,
hydroxyproline, phosphoserine and phosphothreonine; and other
unusual amino acids including, but not limited to, 2-aminoadipic
acid, hydroxylysine, isodesmosine, nor-valine, nor-leucine and
ornithine. Furthermore, the term "amino acid" includes both D- and
L-amino acids.
Table 1 non-conventional or modified amino acids which can be used
with the present invention.
TABLE-US-00003 TABLE 1 Non-conventional amino Non-conventional
amino acid Code acid Code .alpha.-aminobutyric acid Abu
L-N-methylalanine Nmala .alpha.-amino-.alpha.-methylbutyrate Mgabu
L-N-methylarginine Nmarg aminocyclopropane- Cpro
L-N-methylasparagine Nmasn Carboxylate L-N-methylaspartic acid
Nmasp aminoisobutyric acid Aib L-N-methylcysteine Nmcys
aminonorbornyl- Norb L-N-methylglutamine Nmgin Carboxylate
L-N-methylglutamic acid Nmglu Cyclohexylalanine Chexa
L-N-methylhistidine Nmhis Cyclopentylalanine Cpen
L-N-methylisolleucine Nmile D-alanine Dal L-N-methylleucine Nmleu
D-arginine Darg L-N-methyllysine Nmlys D-aspartic acid Dasp
L-N-methylmethionine Nmmet D-cysteine Dcys L-N-methylnorleucine
Nmnle D-glutamine Dgln L-N-methylnorvaline Nmnva D-glutamic acid
Dglu L-N-methylornithine Nmorn D-histidine Dhis
L-N-methylphenylalanine Nmphe D-isoleucine Dile L-N-methylproline
Nmpro D-leucine Dleu L-N-methylserine Nmser D-lysine Dlys
L-N-methylthreonine Nmthr D-methionine Dmet L-N-methyltryptophan
Nmtrp D-ornithine Dorn L-N-methyltyrosine Nmtyr D-phenylalanine
Dphe L-N-methylvaline Nmval D-proline Dpro L-N-methylethylglycine
Nmetg D-serine Dser L-N-methyl-t-butylglycine Nmtbug D-threonine
Dthr L-norleucine Nle D-tryptophan Dtrp L-norvaline Nva D-tyrosine
Dtyr .alpha.-methyl-aminoisobutyrate Maib D-valine Dval
.alpha.-methyl-.gamma.-aminobutyrate Mgabu D-.alpha.-methylalanine
Dmala .alpha.-methylcyclohexylalanine Mchexa
D-.alpha.-methylarginine Dmarg .alpha.-methylcyclopentylalanine
Mcpen D-.alpha.-methylasparagine Dmasn
.alpha.-methyl-.alpha.-napthylalanine Man- ap
D-.alpha.-methylaspartate Dmasp .alpha.-methylpenicillamine Mpen
D-.alpha.-methylcysteine Dmcys N-(4-aminobutyl)glycine Nglu
D-.alpha.-methylglutamine Dmgln N-(2-aminoethyl)glycine Naeg
D-.alpha.-methylhistidine Dmhis N-(3-aminopropyl)glycine Norn
D-.alpha.-methylisoleucine Dmile N-amino-.alpha.-methylbutyrate
Nmaabu D-.alpha.-methylleucine Dmleu .alpha.-napthylalanine Anap
D-.alpha.-methyllysine Dmlys N-benzylglycine Nphe
D-.alpha.-methylmethionine Dmmet N-(2-carbamylethyl)glycine Ngln
D-.alpha.-methylornithine Dmorn N-(carbamylmethyl)glycine Nasn
D-.alpha.-methylphenylalanine Dmphe N-(2-carboxyethyl)glycine Nglu
D-.alpha.-methylproline Dmpro N-(carboxymethyl)glycine Nasp
D-.alpha.-methylserine Dmser N-cyclobutylglycine Ncbut
D-.alpha.-methylthreonine Dmthr N-cycloheptylglycine Nchep
D-.alpha.-methyltryptophan Dmtrp N-cyclohexylglycine Nchex
D-.alpha.-methyltyrosine Dmty N-cyclodecylglycine Ncdec
D-.alpha.-methylvaline Dmval N-cyclododeclglycine Ncdod
D-.alpha.-methylalnine Dnmala N-cyclooctylglycine Ncoct
D-.alpha.-methylarginine Dnmarg N-cyclopropylglycine Ncpro
D-.alpha.-methylasparagine Dnmasn N-cycloundecylglycine Ncund
D-.alpha.-methylasparatate Dnmasp N-(2,2-diphenylethyl)glycine Nbhm
D-.alpha.-methylcysteine Dnmcys N-(3,3-diphenylpropyl)glycine Nbhe
D-N-methylleucine Dnmleu N-(3-indolylyethyl) glycine Nhtrp
D-N-methyllysine Dnmlys N-methyl-.gamma.-aminobutyrate Nmgabu
N-methylcyclohexylalanine Nmchexa D-N-methylmethionine Dnmmet
D-N-methylornithine Dnmorn N-methylcyclopentylalanine Nmcpen
N-methylglycine Nala D-N-methylphenylalanine Dnmphe
N-methylaminoisobutyrate Nmaib D-N-methylproline Dnmpro
N-(1-methylpropyl)glycine Nile D-N-methylserine Dnmser
N-(2-methylpropyl)glycine Nile D-N-methylserine Dnmser
N-(2-methylpropyl)glycine Nleu D-N-methylthreonine Dnmthr
D-N-methyltryptophan Dnmtrp N-(1-methylethyl)glycine Nva
D-N-methyltyrosine Dnmtyr N-methyla-napthylalanine Nmanap
D-N-methylvaline Dnmval N-methylpenicillamine Nmpen
.gamma.-aminobutyric acid Gabu N-(p-hydroxyphenyl)glycine Nhtyr
L-t-butylglycine Tbug N-(thiomethyl)glycine Ncys L-ethylglycine Etg
Penicillamine Pen L-homophenylalanine Hphe L-.alpha.-methylalanine
Mala L-.alpha.-methylarginine Marg L-.alpha.-methylasparagine Masn
L-.alpha.-methylaspartate Masp L-.alpha.-methyl-t-butylglycine
Mtbug L-.alpha.-methylcysteine Mcys L-methylethylglycine Metg
L-.alpha.-methylglutamine Mgln L-.alpha.-methylglutamate Mglu
L-.alpha.-methylhistidine Mhis L-.alpha.-methylhomo phenylalanine
Mhphe L-.alpha.-methylisoleucine Mile N-(2-methylthioethyl)glycine
Nmet D-N-methylglutamine Dnmgln N-(3-guanidinopropyl)glycine Narg
D-N-methylglutamate Dnmglu N-(1-hydroxyethyl)glycine Nthr
D-N-methylhistidine Dnmhis N-(hydroxyethyl)glycine Nser
D-N-methylisoleucine Dnmile N-(imidazolylethyl)glycine Nhis
D-N-methylleucine Dnmleu N-(3-indolylyethyl)glycine Nhtrp
D-N-methyllysine Dnmlys N-methyl-.gamma.-aminobutyrate Nmgabu
N-methylcyclohexylalanine Nmchexa D-N-methylmethionine Dnmmet
D-N-methylornithine Dnmorn N-methylcyclopentylalanine Nmcpen
N-methylglycine Nala D-N-methylphenylalanine Dnmphe
N-methylaminoisobutyrate Nmaib D-N-methylproline Dnmpro
N-(1-methylpropyl)glycine Nile D-N-methylserine Dnmser
N-(2-methylpropyl)glycine Nleu D-N-methylthreonine Dnmthr
D-N-methyltryptophan Dnmtrp N-(1-methylethyl)glycine Nval
D-N-methyltyrosine Dnmtyr N-methyla-napthylalanine Nmanap
D-N-methylvaline Dnmval N-methylpenicillamine Nmpen
.gamma.-aminobutyric acid Gabu N-(p-hydroxyphenyl)glycine Nhtyr
L-t-butylglycine Tbug N-(thiomethyl)glycine Ncys L-ethylglycine Etg
Penicillamine Pen L-homophenylalanine Hphe L-.alpha.-methylalanine
Mala L-.alpha.-methylarginine Marg L-.alpha.-methylasparagine Masn
L-.alpha.-methylaspartate Masp L-.alpha.-methyl-t-butylglycine
Mtbug L-.alpha.-methylcysteine Mcys L-methylethylglycine Metg
L-.alpha.-methylglutamine Mgln L-.alpha.-methylglutamate Mglu
L-.alpha.-methylhistidine Mhis L-.alpha.-methylhomophenylalanine
Mhphe L-.alpha.-methylisoleucine Mile N-(2-methylthioethyl)glycine
Nmet L-.alpha.-methylleucine Mleu L-.alpha.-methyllysine Mlys
L-.alpha.-methylmethionine Mmet L-.alpha.-methylnorleucine Mnle
L-.alpha.-methylnorvaline Mnva L-.alpha.-methylornithine Morn
L-.alpha.-methylphenylalanine Mphe L-.alpha.-methylproline Mpro
L-.alpha.-methylserine mser L-.alpha.-methylthreonine Mthr
L-.alpha.-methylvaline Mtrp L-.alpha.-methyltyrosine Mtyr
L-.alpha.-methylleucine Mval L-N-methylhomophenylalanine Nmhphe
Nnbhm N-(N-(2,2-diphenylethyl) N-(N-(3,3-diphenylpropyl)
carbamylmethyl-glycine Nnbhm carbamylmethyl(1)glycine Nnbhe
1-carboxy-1-(2,2-diphenylethylamino) Nmbc cyclopropane
Since the peptides of the present invention are preferably utilized
in diagnostics which require the peptides to be in soluble form,
the peptides of the present invention preferably include one or
more non-natural or natural polar amino acids, including but not
limited to serine and threonine which are capable of increasing
peptide solubility due to their hydroxyl-containing side chain.
The peptides of the present invention are preferably utilized in a
linear form, although it will be appreciated that in cases where
cyclicization does not severely interfere with peptide
characteristics, cyclic forms of the peptide can also be
utilized.
The peptides of present invention can be biochemically synthesized
such as by using standard solid phase techniques. These methods
include exclusive solid phase synthesis well known in the art,
partial solid phase synthesis methods, fragment condensation,
classical solution synthesis. These methods are preferably used
when the peptide is relatively short (i.e., 10 kDa) and/or when it
cannot be produced by recombinant techniques (i.e., not encoded by
a nucleic acid sequence) and therefore involves different
chemistry.
Synthetic peptides can be purified by preparative high performance
liquid chromatography and the composition of which can be confirmed
via amino acid sequencing.
In cases where large amounts of the peptides of the present
invention are desired, the peptides of the present invention can be
generated using recombinant techniques such as described by Bitter
et al., (1987) Methods in Enzymol. 153:516-544, Studier et al.
(1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984) Nature
310:511-514, Takamatsu et al. (1987) EMBO J. 6:307-311, Coruzzi et
al. (1984) EMBO J. 3:1671-1680 and Brogli et al., (1984) Science
224:838-843, Gurley et al. (1986) Mol. Cell. Biol. 6:559-565 and
Weissbach & Weissbach, 1988, Methods for Plant Molecular
Biology, Academic Press, NY, Section VIII, pp 421-463 and also as
described above.
Antibodies
"Antibody" refers to a polypeptide ligand that is preferably
substantially encoded by an immunoglobulin gene or immunoglobulin
genes, or fragments thereof, which specifically binds and
recognizes an epitope (e.g., an antigen). The recognized
immunoglobulin genes include the kappa and lambda light chain
constant region genes, the alpha, gamma, delta, epsilon and mu
heavy chain constant region genes, and the myriad-immunoglobulin
variable region genes. Antibodies exist, e.g., as intact
immunoglobulins or as a number of well characterized fragments
produced by digestion with various peptidases. This includes, e.g.,
Fab' and F(ab)'.sub.2 fragments. The term "antibody," as used
herein, also includes antibody fragments either produced by the
modification of whole antibodies or those synthesized de novo using
recombinant DNA methodologies. It also includes polyclonal
antibodies, monoclonal antibodies, chimeric antibodies, humanized
antibodies, or single chain antibodies. "Fc" portion of an antibody
refers to that portion of an immunoglobulin heavy chain that
comprises one or more heavy chain constant region domains, CH1, CH2
and CH3, but does not include the heavy chain variable region.
The functional fragments of antibodies, such as Fab, F(ab')2, and
Fv that are capable of binding to macrophages, are described as
follows: (1) Fab, the fragment which contains a monovalent
antigen-binding fragment of an antibody molecule, can be produced
by digestion of whole antibody with the enzyme papain to yield an
intact light chain and a portion of one heavy chain; (2) Fab', the
fragment of an antibody molecule that can be obtained by treating
whole antibody with pepsin, followed by reduction, to yield an
intact light chain and a portion of the heavy chain; two Fab'
fragments are obtained per antibody molecule; (3) (Fab')2, the
fragment of the antibody that can be obtained by treating whole
antibody with the enzyme pepsin without subsequent reduction;
F(ab')2 is a dimer of two Fab' fragments held together by two
disulfide bonds; (4) Fv, defined as a genetically engineered
fragment containing the variable region of the light chain and the
variable region of the heavy chain expressed as two chains; and (5)
Single chain antibody ("SCA"), a genetically engineered molecule
containing the variable region of the light chain and the variable
region of the heavy chain, linked by a suitable polypeptide linker
as a genetically fused single chain molecule.
Methods of producing polyclonal and monoclonal antibodies as well
as fragments thereof are well known in the art (See for example,
Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring
Harbor Laboratory, New York, 1988, incorporated herein by
reference).
Antibody fragments according to the present invention can be
prepared by proteolytic hydrolysis of the antibody or by expression
in E. coli or mammalian cells (e.g. Chinese hamster ovary cell
culture or other protein expression systems) of DNA encoding the
fragment. Antibody fragments can be obtained by pepsin or papain
digestion of whole antibodies by conventional methods. For example,
antibody fragments can be produced by enzymatic cleavage of
antibodies with pepsin to provide a 5S fragment denoted F(ab')2.
This fragment can be further cleaved using a thiol reducing agent,
and optionally a blocking group for the sulfhydryl groups resulting
from cleavage of disulfide linkages, to produce 3.5S Fab'
monovalent fragments. Alternatively, an enzymatic cleavage using
pepsin produces two monovalent Fab' fragments and an Fc fragment
directly. These methods are described, for example, by Goldenberg,
U.S. Pat. Nos. 4,036,945 and 4,331,647, and references contained
therein, which patents are hereby incorporated by reference in
their entirety. See also Porter, R. R. [Biochem. J. 73: 119-126
(1959)]. Other methods of cleaving antibodies, such as separation
of heavy chains to form monovalent light-heavy chain fragments,
further cleavage of fragments, or other enzymatic, chemical, or
genetic techniques may also be used, so long as the fragments bind
to the antigen that is recognized by the intact antibody.
Fv fragments comprise an association of VH and VL chains. This
association may be noncovalent, as described in Inbar et al. [Proc.
Nat'l Acad. Sci. USA 69:2659-62 (19720]. Alternatively, the
variable chains can be linked by an intermolecular disulfide bond
or crosslinked by chemicals such as glutaraldehyde. Preferably, the
Fv fragments comprise VH and VL chains connected by a peptide
linker. These single-chain antigen binding proteins (sFv) are
prepared by constructing a structural gene comprising DNA sequences
encoding the VH and VL domains connected by an oligonucleotide. The
structural gene is inserted into an expression vector, which is
subsequently introduced into a host cell such as E. coli. The
recombinant host cells synthesize a single polypeptide chain with a
linker peptide bridging the two V domains. Methods for producing
sFvs are described, for example, by [Whitlow and Filpula, Methods
2: 97-105 (1991); Bird et al., Science 242:423-426 (1988); Pack et
al., Bio/Technology 11:1271-77 (1993); and U.S. Pat. No. 4,946,778,
which is hereby incorporated by reference in its entirety.
Another form of an antibody fragment is a peptide coding for a
single complementarity-determining region (CDR). CDR peptides
("minimal recognition units") can be obtained by constructing genes
encoding the CDR of an antibody of interest. Such genes are
prepared, for example, by using the polymerase chain reaction to
synthesize the variable region from RNA of antibody-producing
cells. See, for example, Larrick and Fry [Methods, 2: 106-10
(1991)].
Humanized forms of non-human (e.g., murine) antibodies are chimeric
molecules of immunoglobulins, immunoglobulin chains or fragments
thereof (such as Fv, Fab, Fab', F(ab') or other antigen-binding
subsequences of antibodies) which contain minimal sequence derived
from non-human immunoglobulin. Humanized antibodies include human
immunoglobulins (recipient antibody) in which residues from a
complementary determining region (CDR) of the recipient are
replaced by residues from a CDR of a non-human species (donor
antibody) such as mouse, rat or rabbit having the desired
specificity, affinity and capacity. In some instances, Fv framework
residues of the human immunoglobulin are replaced by corresponding
non-human residues. Humanized antibodies may also comprise residues
which are found neither in the recipient antibody nor in the
imported CDR or framework sequences. In general, the humanized
antibody will comprise substantially all of at least one, and
typically two, variable domains, in which all or substantially all
of the CDR regions correspond to those of a non-human
immunoglobulin and all or substantially all of the FR regions are
those of a human immunoglobulin consensus sequence. The humanized
antibody optimally also will comprise at least a portion of an
immunoglobulin constant region (Fc), typically that of a human
immunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann
et al., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct.
Biol., 2:593-596 (1992)].
Methods for humanizing non-human antibodies are well known in the
art. Generally, a humanized antibody has one or more amino acid
residues introduced into it from a source which is non-human. These
non-human amino acid residues are often referred to as import
residues, which are typically taken from an import variable domain.
Humanization can be essentially performed following the method of
Winter and co-workers [Jones et al., Nature, 321:522-525 (1986);
Riechmann et al., Nature 332:323-327 (1988); Verhoeyen et al.,
Science, 239:1534-1536 (1988)], by substituting rodent CDRs or CDR
sequences for the corresponding sequences of a human antibody.
Accordingly, such humanized antibodies are chimeric antibodies
(U.S. Pat. No. 4,816,567), wherein substantially less than an
intact human variable domain has been substituted by the
corresponding sequence from a non-human species. In practice,
humanized antibodies are typically human antibodies in which some
CDR residues and possibly some FR residues are substituted by
residues from analogous sites in rodent antibodies.
Human antibodies can also be produced using various techniques
known in the art, including phage display libraries [Hoogenboom and
Winter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol.,
222:581 (1991)]. The techniques of Cole et al. and Boerner et al.
are also available for the preparation of human monoclonal
antibodies (Cole et al., Monoclonal Antibodies and Cancer Therapy,
Alan R. Liss, p. 77 (1985) and Boerner et al., J. Immunol.,
147(1):86-95 (1991)]. Similarly, human antibodies can be made by
introduction of human immunoglobulin loci into transgenic animals,
e.g., mice in which the endogenous immunoglobulin genes have been
partially or completely inactivated. Upon challenge, human antibody
production is observed, which closely resembles that seen in humans
in all respects, including gene rearrangement, assembly, and
antibody repertoire. This approach is described, for example, in
U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126;
5,633,425; 5,661,016, and in the following scientific publications:
Marks et al., Bio/Technology 10: 779-783 (1992); Lonberg et al.,
Nature 368: 856-859 (1994); Morrison, Nature 368 812-13 (1994);
Fishwild et al., Nature Biotechnology 14, 845-51 (1996); Neuberger,
Nature Biotechnology 14: 826 (1996); and Lonberg and Huszar,
Intern. Rev. Immunol. 13, 65-93 (1995).
Preferably, the antibody of this aspect of the present invention
specifically binds at least one epitope of the polypeptide variants
of the present invention. As used herein, the term "epitope" refers
to any antigenic determinant on an antigen to which the paratope of
an antibody binds.
Epitopic determinants usually consist of chemically active surface
groupings of molecules such as amino acids or carbohydrate side
chains and usually have specific three dimensional structural
characteristics, as well as specific charge characteristics.
Optionally, a unique epitope may be created in a variant due to a
change in one or more post-translational modifications, including
but not limited to glycosylation and/or phosphorylation, as
described below. Such a change may also cause a new epitope to be
created, for example through removal of glycosylation at a
particular site.
An epitope according to the present invention may also optionally
comprise part or all of a unique sequence portion of a variant
according to the present invention in combination with at least one
other portion of the variant which is not contiguous to the unique
sequence portion in the linear polypeptide itself, yet which are
able to form an epitope in combination. One or more unique sequence
portions may optionally combine with one or more other
non-contiguous portions of the variant (including a portion which
may have high homology to a portion of the known protein) to form
an epitope.
Immunoassays
In another embodiment of the present invention, an immunoassay can
be used to qualitatively or quantitatively detect and analyze
markers in a sample. This method comprises: providing an antibody
that specifically binds to a marker; contacting a sample with the
antibody; and detecting the presence of a complex of the antibody
bound to the marker in the sample.
To prepare an antibody that specifically binds to a marker,
purified protein markers can be used. Antibodies that specifically
bind to a protein marker can be prepared using any suitable methods
known in the art.
After the antibody is provided, a marker can be detected and/or
quantified using any of a number of well recognized immunological
binding assays. Useful assays include, for example, an enzyme
immune assay (EIA) such as enzyme-linked immunosorbent assay
(ELISA), a radioimmune assay (RIA), a Western blot assay, or a slot
blot assay see, e.g., U.S. Pat. Nos. 4,366,241; 4,376,110;
4,517,288; and 4,837,168). Generally, a sample obtained from a
subject can be contacted with the antibody that specifically binds
the marker.
Optionally, the antibody can be fixed to a solid support to
facilitate washing and subsequent isolation of the complex, prior
to contacting the antibody with a sample. Examples of solid
supports include but are not limited to glass or plastic in the
form of, e.g., a microtiter plate, a stick, a bead, or a microbead.
Antibodies can also be attached to a solid support.
After incubating the sample with antibodies, the mixture is washed
and the antibody-marker complex formed can be detected. This can be
accomplished by incubating the washed mixture with a detection
reagent. Alternatively, the marker in the sample can be detected
using an indirect assay, wherein, for example, a second, labeled
antibody is used to detect bound marker-specific antibody, and/or
in a competition or inhibition assay wherein, for example, a
monoclonal antibody which binds to a distinct epitope of the marker
are incubated simultaneously with the mixture.
Throughout the assays, incubation and/or washing steps may be
required after each combination of reagents. Incubation steps can
vary from about 5 seconds to several hours, preferably from about 5
minutes to about 24 hours. However, the incubation time will depend
upon the assay format, marker, volume of solution, concentrations
and the like. Usually the assays will be carried out at ambient
temperature, although they can be conducted over a range of
temperatures, such as 10.degree. C. to 40.degree. C.
The immunoassay can be used to determine a test amount of a marker
in a sample from a subject. First, a test amount of a marker in a
sample can be detected using the immunoassay methods described
above. If a marker is present in the sample, it will form an
antibody-marker complex with an antibody that specifically binds
the marker under suitable incubation conditions described above.
The amount of an antibody-marker complex can optionally be
determined by comparing to a standard. As noted above, the test
amount of marker need not be measured in absolute units, as long as
the unit of measurement can be compared to a control amount and/or
signal.
Preferably used are antibodies which specifically interact with the
polypeptides of the present invention and not with wild type
proteins or other isoforms thereof, for example. Such antibodies
are directed, for example, to the unique sequence portions of the
polypeptide variants of the present invention, including but not
limited to bridges, heads, tails and insertions described in
greater detail below. Preferred embodiments of antibodies according
to the present invention are described in greater detail with
regard to the section entitled "Antibodies".
Radio-immunoassay (RIA): In one version, this method involves
precipitation of the desired substrate and in the methods detailed
hereinbelow, with a specific antibody and radiolabelled antibody
binding protein (e.g., protein A labeled with I.sup.125)
immobilized on a precipitable carrier such as agarose beads. The
number of counts in the precipitated pellet is proportional to the
amount of substrate.
In an alternate version of the RIA, a labeled substrate and an
unlabelled antibody binding protein are employed. A sample
containing an unknown amount of substrate is added in varying
amounts. The decrease in precipitated counts from the labeled
substrate is proportional to the amount of substrate in the added
sample.
Enzyme linked immunosorbent assay (ELISA): This method involves
fixation of a sample (e.g., fixed cells or a proteinaceous
solution) containing a protein substrate to a surface such as a
well of a microtiter plate. A substrate specific antibody coupled
to an enzyme is applied and allowed to bind to the substrate.
Presence of the antibody is then detected and quantitated by a
colorimetric reaction employing the enzyme coupled to the antibody.
Enzymes commonly employed in this method include horseradish
peroxidase and alkaline phosphatase. If well calibrated and within
the linear range of response, the amount of substrate present in
the sample is proportional to the amount of color produced. A
substrate standard is generally employed to improve quantitative
accuracy.
Western blot: This method involves separation of a substrate from
other protein by means of an acrylamide gel followed by transfer of
the substrate to a membrane (e.g., nylon or PVDF). Presence of the
substrate is then detected by antibodies specific to the substrate,
which are in turn detected by antibody binding reagents. Antibody
binding reagents may be, for example, protein A, or other
antibodies. Antibody binding reagents may be radiolabelled or
enzyme linked as described hereinabove. Detection may be by
autoradiography, calorimetric reaction or chemiluminescence. This
method allows both quantitation of an amount of substrate and
determination of its identity by a relative position on the
membrane which is indicative of a migration distance in the
acrylamide gel during electrophoresis.
Immunohistochemical analysis: This method involves detection of a
substrate in situ in fixed cells by substrate specific antibodies.
The substrate specific antibodies may be enzyme linked or linked to
fluorophores. Detection is by microscopy and subjective evaluation.
If enzyme linked antibodies are employed, a calorimetric reaction
may be required.
Fluorescence activated cell sorting (FACS): This method involves
detection of a substrate in situ in cells by substrate specific
antibodies. The substrate specific antibodies are linked to
fluorophores. Detection is by means of a cell sorting machine which
reads the wavelength of light emitted from each cell as it passes
through a light beam. This method may employ two or more antibodies
simultaneously.
Radio-imaging Methods
These methods include but are not limited to, positron emission
tomography (PET) single photon emission computed tomography
(SPECT). Both of these techniques are noninvasive, and can be used
to detect and/or measure a wide variety of tissue events and/or
functions, such as detecting cancerous cells for example. Unlike
PET, SPECT can optionally be used with two labels simultaneously.
SPECT has some other advantages as well, for example with regard to
cost and the types of labels that can be used. For example, U.S.
Pat. No. 6,696,686 describes the use of SPECT for detection of
breast cancer, and is hereby incorporated by reference as if fully
set forth herein.
Display Libraries
According to still another aspect of the present invention there is
provided a display library comprising a plurality of display
vehicles (such as phages, viruses or bacteria) each displaying at
least 6, at least 7, at least 8, at least 9, at least 10, 10-15,
12-17, 15-20, 15-30 or 20-50 consecutive amino acids derived from
the polypeptide sequences of the present invention.
Methods of constructing such display libraries are well known in
the art. Such methods are described in, for example, Young A C, et
al., "The three-dimensional structures of a polysaccharide binding
antibody to Cryptococcus neoformans and its complex with a peptide
from a phage display library: implications for the identification
of peptide mimotopes" J Mol Biol 1997 Dec. 12; 274(4):622-34;
Giebel L B et al. "Screening of cyclic peptide phage libraries
identifies ligands that bind streptavidin with high affinities"
Biochemistry 1995 Nov. 28; 34(47):15430-5; Davies E L et al.,
"Selection of specific phage-display antibodies using libraries
derived from chicken immunoglobulin genes" J Immunol Methods 1995
Oct. 12; 186(1):125-35; Jones C R T al. "Current trends in
molecular recognition and bioseparation" J Chromatogr A 1995 Jul.
14; 707(1):3-22; Deng S J et al. "Basis for selection of improved
carbohydrate-binding single-chain antibodies from synthetic gene
libraries" Proc Natl Acad Sci USA 1995 May 23; 92(11):4992-6; and
Deng S J et al. "Selection of antibody single-chain variable
fragments with improved carbohydrate binding by phage display" J
Biol Chem 1994 Apr. 1; 269(13):9533-8, which are incorporated
herein by reference.
The following sections relate to Candidate Marker Examples (first
section) and to Experimental Data for these Marker Examples (second
section). It should be noted that Table numbering is restarted
within each section.
Candidate Marker Examples Section
This section relates to examples of sequences according to the
present invention, including illustrative methods of selection
thereof.
Description of the Methodology Undertaken to Uncover the
Biomolecular Sequences of the Present Invention
Human ESTs and cDNAs were obtained from GenBank versions 136 (Jun.
15, 2003 ftp dot ncbi dot nih dot gov/genbank/release dot
notes/gb136 dot release dot notes); NCBI genome assembly of April
2003; RefSeq sequences from June 2003; Genbank version 139
(December 2003); Human Genome from NCBI (Build 34) (from October
2003); and RefSeq sequences from December 2003 dot With regard to
GenBank sequences, the human EST sequences from the EST (GBEST)
section and the human mRNA sequences from the primate (GBPRI)
section were used; also the human nucleotide RefSeq mRNA sequences
were used (see for example dot ncbi dot nlm dot nih dot
gov/Genbank/GenbankOverview dot html and for a reference to the EST
section, see dot ncbi dot nlm dot nih dot gov/dbEST/; a general
reference to dbEST, the EST database in GenBank, may be found in
Boguski et al, Nat Genet. 1993 August; 4(4):332-3; all of which are
hereby incorporated by reference as if fully set forth herein).
Novel splice variants were predicted using the LEADS clustering and
assembly system as described in Sorek, R., Ast, G. & Graur, D.
Alu-containing exons are alternatively spliced. Genome Res 12,
1060-7 (2002); U.S. Pat. No. 6,625,545; and U.S. patent application
Ser. No. 10/426,002, published as US20040101876 on May 27, 2004;
all of which are hereby incorporated by reference as if fully set
forth herein. Briefly, the software cleans the expressed sequences
from repeats, vectors and immunoglobulins. It then aligns the
expressed sequences to the genome taking alternatively splicing
into account and clusters overlapping expressed sequences into
"clusters" that represent genes or partial genes.
These were annotated using the GeneCarta (Compugen, Tel-Aviv,
Israel) platform. The GeneCarta platform includes a rich pool of
annotations, sequence information (particularly of spliced
sequences), chromosomal information, alignments, and additional
information such as SNPs, gene ontology terms, expression profiles,
functional analyses, detailed domain structures, known and
predicted proteins and detailed homology reports.
A brief explanation is provided with regard to the method of
selecting the candidates. However, it should be noted that this
explanation is provided for descriptive purposes only, and is not
intended to be limiting in any way. The potential markers were
identified by a computational process that was designed to find
genes and/or their splice variants that are specifically expressed
in cardiac tissue, as opposed to other types of tissues and also
particularly as opposed to muscle tissue, by using databases of
expressed sequences. Various parameters related to the information
in the EST libraries, determined according to classification by
library annotation, were used to assist in locating genes and/or
splice variants thereof that are specifically and/or differentially
expressed in heart tissues. The detailed description of the
selection method and of these parameters is presented in Example 1
below.
EXAMPLE 1
Identification of Differentially Expressed Gene
Products--Algorithm
In order to distinguish between differentially expressed gene
products and constitutively expressed genes (i.e., house keeping
genes), an algorithm based on an analysis of frequencies was
configured. A specific algorithm for identification of transcripts
specifically expressed in heart tissue is described
hereinbelow.
EST Analysis
ESTs were taken from the following main sources: libraries
contained in Genbank version 136 (Jun. 15, 2003
ftp.ncbi.nih.gov/genbank/release.notes/gb136.release.notes) and
Genbank version 139 (December 2003); and from the LifeSeq library
of Incyte Corporation (ESTs only; Wilmington, Del., USA). With
regard to GenBank sequences, the human EST sequences from the EST
(GBEST) section were used.
Library annotation--EST libraries were manually classified
according to: 1. Tissue origin 2. Biological source--Examples of
frequently used biological sources for construction of EST
libraries include cancer cell-lines; normal tissues; cancer
tissues; foetal tissues; and others such as normal cell lines and
pools of normal cell-lines, cancer cell-lines and combinations
thereof. A specific description of abbreviations used below with
regard to these tissues/cell lines etc is given above. 3. Protocol
of library construction--various methods are known in the art for
library construction including normalized library construction;
non-normalized library construction; subtracted libraries; ORESTES
and others (described in the annotation available in Genbank). It
will be appreciated that at times the protocol of library
construction is not indicated in the information available about
that library.
The following rules were followed:
EST libraries originating from identical biological samples were
considered as a single library.
EST libraries which included above-average levels of contamination,
such as DNA contamination for example, were eliminated. The
presence of such contamination was determined as follows. For each
library, the number of unspliced ESTs that are not fully contained
within other spliced sequences was counted. If the percentage of
such sequences (as compared to all other sequences) was at least 4
standard deviations above the average for all libraries being
analyzed, this library was tagged as being contaminated and was
eliminated from further consideration in the below analysis (see
also Sorek, R. & Safer, H. M. A novel algorithm for
computational identification of contaminated EST libraries. Nucleic
Acids Res 31, 1067-74 (2003) for further details).
Clusters (genes) having at least five sequences including at least
two sequences from the tissue of interest were analyzed. Splice
variants were identified by using the LEADS software package as
described above.
EXAMPLE 2
Identification of Heart Tissue Specific Genes
For detection of heart tissue specific clusters, heart tissue
libraries/sequences were compared to the total number of
libraries/sequences in the cluster and in Genebank, and to the
relevant numbers for muscle tissue libraries/sequences. Statistical
tools were employed to identify clusters that were heart tissue
specific, both as compared to all other tissues and also in
comparison to muscle tissue.
The algorithm--for each tested tissue T and for each tested cluster
the following were examined:
1. Each cluster includes at least 2 libraries from the tissue T. At
least 3 clones (weighed--as described above) from tissue T in the
cluster;
2. The following equation was then used to determine heart
tissue-specific expression as compared to expression in all tissue
types for a particular cluster:
##EQU00001## in which n is the total number of ESTs available for a
cluster, while N is the total number of ESTs available in all of
the libraries considered in the analysis (effectively all ESTs in
Genbank, except for those that were rejected as belonging to
contaminated libraries). This ratio was preferably set to be at
least about 8, although optionally the ratio could be set to be at
least about 5.
3. The following equation was then used to determine heart
tissue-specific expression vs. expression in skeletal muscle tissue
for a particular cluster:
##EQU00002## in which t represents the number of heart
tissue-specific ESTs for the cluster, while T is the number of all
heart tissue-specific ESTs in the analysis; m is the number of
skeletal muscle tissue-specific ESTs for the cluster, while M is
the number of all skeletal muscle tissue-specific ESTs in the
analysis. This ratio was preferably set to be at least about 4,
although optionally the ratio could be set to be at least about
2.
4. Fisher exact test P-values were computed for weighted clone
counts to check that the counts are statistically significant
according to the following function: F(t,T,n,N) which is the
probability of a cluster actually being overexpressed in heart
tissue, as compared to its overall level of expression. The P-value
was preferably set to be less than about 1e-5, although optionally
it could be set to be less than about 1e-3.
The results obtained are explained in greater detail for each
marker below.
Actual Marker Examples
The following examples relate to specific actual marker examples.
It should be noted that Table numbering is restarted within each
example related to a particular Cluster, as indicated by the titles
below.
EXAMPLES SECTION
This Section relates to Examples of sequences according to the
present invention, including experiments involving these sequences,
and illustrative, non-limiting examples of methods, assays and uses
thereof. The materials and experimental procedures are explained
first, as all experiments used them as a basis for the work that
was performed.
The markers of the present invention were tested with regard to
their expression in various heart and non-heart tissue samples.
Unless otherwise noted, all experimental data relates to variants
of the present invention, named according to the segment being
tested (as expression was tested through RT-PCR as described). A
description of the samples used in the panel is provided in Table 1
below. Tests were then performed as described in the Examples
below.
TABLE-US-00004 TABLE 1 Tissue samples in testing panel Lot no.
Source Tissue Pathology Sex/Age 1-Am-Colon (C71) 071P10B Ambion
Colon PM F/43 2-B-Colon (C69) A411078 Biochain Colon PM-Pool of 10
M&F 3-Cl-Colon (C70) 1110101 Clontech Colon PM-Pool of 3
M&F 4-Am-Small Intestine 091P0201A Ambion Small Intestine PM
M/75 5-B-Small Intestine A501158 Biochain Small Intestine PM M/63
6-B-Rectum A605138 Biochain Rectum PM M/25 7-B-Rectum A610297
Biochain Rectum PM M/24 8-B-Rectum A610298 Biochain Rectum PM M/27
9-Am-Stomach 110P04A Ambion Stomach PM M/16 10-B-Stomach A501159
Biochain Stomach PM M/24 11-B-Esophagus A603814 Biochain Esophagus
PM M/26 12-B-Esophagus A603813 Biochain Esophagus PM M/41
13-Am-Pancreas 071P25C Ambion Pancreas PM M/25 14-CG-Pancreas
CG-255-2 Ichilov Pancreas PM M/75 15-B-Lung A409363 Biochain Lung
PM F/26 16-Am-Lung (L93) 111P0103A Ambion Lung PM F/61 17-B-Lung
(L92) A503204 Biochain Lung PM M/28 18-Am-Ovary (O47) 061P43A
Ambion Ovary PM F/16 19-B-Ovary (O48) A504087 Biochain Ovary PM
F/51 20-B-Ovary (O46) A504086 Biochain Ovary PM F/41 21-Am-Cervix
101P0101A Ambion Cervix PM F/40 22-B-Cervix A408211 Biochain Cervix
PM F/36 23-B-Cervix A504089 Biochain Cervix PM-Pool of 5 M&F
24-B-Uterus A411074 Biochain Uterus PM-Pool of 10 M&F
25-B-Uterus A409248 Biochain Uterus PM F/43 26-B-Uterus A504090
Biochain Uterus PM-Pool of 5 M&F 27-B-Bladder A501157 Biochain
Bladder PM M/29 28-Am-Bladder 071P02C Ambion Bladder PM M/20
29-B-Bladder A504088 Biochain Bladder PM-Pool of 5 M&F
30-Am-Placenta 021P33A Ambion Placenta PB F/33 31-B-Placenta
A410165 Biochain Placenta PB F/26 32-B-Placenta A411073 Biochain
Placenta PB-Pool of 5 M&F 33-B-Breast (B59) A607155 Biochain
Breast PM F/36 34-Am-Breast (B63) 26486 Ambion Breast PM F/43
35-Am-Breast (B64) 23036 Ambion Breast PM F/57 36-Cl-Prostate (P53)
1070317 Clontech Prostate PB-Pool of 47 M&F 37-Am-Prostate
(P42) 061P04A Ambion Prostate PM M/47 38-Am-Prostate (P59) 25955
Ambion Prostate PM M/62 39-Am-Testis 111P0104A Ambion Testis PM
M/25 40-B-Testis A411147 Biochain Testis PM M/74 41-Cl-Testis
1110320 Clontech Testis PB-Pool of 45 M&F 42-CG-Adrenal
CG-184-10 Ichilov Adrenal PM F/81 43-B-Adrenal A610374 Biochain
Adrenal PM F/83 44-B-Heart A411077 Biochain Heart PB-Pool of 5
M&F 45-CG-Heart CG-255-9 Ichilov Heart PM M/75 46-CG-Heart
CG-227-1 Ichilov Heart PM F/36 47-Am-Liver 081P0101A Ambion Liver
PM M/64 48-CG-Liver CG-93-3 Ichilov Liver PM F/19 49-CG-Liver
CG-124-4 Ichilov Liver PM F/34 50-Cl-BM 1110932 Clontech Bone
Marrow PM-Pool of 8 M&F 51-CGEN-Blood WBC#5 CGEN Blood M
52-CGEN-Blood WBC#4 CGEN Blood M 53-CGEN-Blood WBC#3 CGEN Blood M
54-CG-Spleen CG-267 Ichilov Spleen PM F/25 55-CG-Spleen 111P0106B
Ambion Spleen PM M/25 56-CG-Spleen A409246 Biochain Spleen PM F/12
56-CG-Thymus CG-98-7 Ichilov Thymus PM F/28 58-Am-Thymus 101P0101A
Ambion Thymus PM M/14 59-B-Thymus A409278 Biochain Thymus PM M/28
60-B-Thyroid A610287 Biochain Thyroid PM M/27 61-B-Thyroid A610286
Biochain Thyroid PM M/24 62-CG-Thyroid CG-119-2 Ichilov Thyroid PM
F/66 63-Cl-Salivary Gland 1070319 Clontech Salivary Gland PM-Pool
of 24 M&F 64-Am-Kidney 111P0101B Ambion Kidney PM-Pool of 14
M&F 65-Cl-Kidney 1110970 Clontech Kidney PM-Pool of 14 M&F
66-B-Kidney A411080 Biochain Kidney PM-Pool of 5 M&F
67-CG-Cerebellum CG-183-5 Ichilov Cerebellum PM M/74
68-CG-Cerebellum CG-212-5 Ichilov Cerebellum PM M/54 69-B-Brain
A411322 Biochain Brain PM M/28 70-Cl-Brain 1120022 Clontech Brain
PM-Pool of 2 M&F 71-B-Brain A411079 Biochain Brain PM-Pool of 2
M&F 72-CG-Brain CG-151-1 Ichilov Brain PM F/86 73-Am-Skeletal
Muscle 101P013A Ambion Skeletal Muscle PM F/28 74-Cl-Skeletal
Muscle 1061038 Clontech Skeletal Muscle PM-Pool of 2 M&F
Materials and Experimental Procedures
RNA preparation--RNA was obtained from Clontech (Franklin Lakes,
N.J. USA 07417, dot clontech dot com), BioChain Inst. Inc.
(Hayward, Calif. 94545 USA dot biochain dot com), ABS (Wilmington,
Del. 19801, USA, dot absbioreagents dot com) or Ambion (Austin,
Tex. 78744 USA, dot ambion dot com). Alternatively, RNA was
generated from tissue samples using TRI-Reagent (Molecular Research
Center), according to Manufacturer's instructions. Tissue and RNA
samples were obtained from patients or from postmortem. Total RNA
samples were treated with DNasel (Ambion) and purified using RNeasy
columns (Qiagen).
RT PCR--Purified RNA (1 .mu.g) was mixed with 150 ng Random Hexamer
primers (Invitrogen) and 500 .mu.M dNTP in a total volume of 15.6
.mu.l. The mixture was incubated for 5 min at 65.degree. C. and
then quickly chilled on ice. Thereafter, 5 .mu.l of 5.times.
SuperscriptII first strand buffer (Invitrogen), 2.4 .mu.l 0.1M DTT
and 40 units RNasin (Promega) were added, and the mixture was
incubated for 10 min at 25.degree. C., followed by further
incubation at 42.degree. C. for 2 min. Then, 1 .mu.l (200 units) of
SuperscriptII (Invitrogen) was added and the reaction (final volume
of 25 .mu.l) was incubated for 50 min at 42.degree. C. and then
inactivated at 70.degree. C. for 15 min. The resulting cDNA was
diluted 1:20 in TE buffer (10 mM Tris pH=8, 1 mM EDTA pH=8).
Real-Time RT-PCR analysis--cDNA (5 .mu.l), prepared as described
above, was used as a template in Real-Time PCR reactions using the
SYBR Green I assay (PE Applied Biosystem) with specific primers and
UNG Enzyme (Eurogentech or ABI or Roche). The amplification was
effected as follows: 50.degree. C. for 2 min, 95.degree. C. for 10
min, and then 40 cycles of 95.degree. C. for 15 sec, followed by
60.degree. C. for 1 min. Detection was performed by using the PE
Applied Biosystem SDS 7000. The cycle in which the reactions
achieved a threshold level (Ct) of fluorescence was registered and
was used to calculate the relative transcript quantity in the RT
reactions. The relative quantity was calculated using the equation
Q=efficiency^.sup.-Ct. The efficiency of the PCR reaction was
calculated from a standard curve, created by using serial dilutions
of several reverse transcription (RT) reactions To minimize
inherent differences in the RT reaction, the resulting relative
quantities were normalized to the geometric mean of the relative
quantities of several housekeeping (HSKP) genes. Schematic summary
of quantitative real-time PCR analysis is presented in FIG. 1. As
shown, the x-axis shows the cycle number. The C.sub.T=Threshold
Cycle point, which is the cycle that the amplification curve
crosses the fluorescence threshold that was set in the experiment.
This point is a calculated cycle number in which PCR products
signal is above the background level (passive dye ROX) and still in
the Geometric/Exponential phase (as shown, once the level of
fluorescence crosses the measurement threshold, it has a
geometrically increasing phase, during which measurements are most
accurate, followed by a linear phase and a plateau phase; for
quantitative measurements, the latter two phases do not provide
accurate measurements). The y-axis shows the normalized reporter
fluorescence. It should be noted that this type of analysis
provides relative quantification.
The sequences of the housekeeping genes measured in all the
examples on normal tissue samples panel were as follows:
TABLE-US-00005 RPL19 (GenBank Accession No. NM_000981 (SEQ ID
NO:437)), RPL19 Forward primer (SEQ ID NO:438):
TGGCAAGAAGAAGGTCTGGTTAG RPL19 Reverse primer (SEQ ID NO:439):
TGATCAGCCCATCTTTGATGAG RPL19-amplicon (SEQ ID NO:440):
TGGCAAGAAGAAGGTCTGGTTAGACCCCAATGAGACCAATGAAATCGCCAATG
CCAACTCCCGTCAGCAGATCCGGAAGCTCATCAAAGATGGGCTGATCA TATA box (GenBank
Accession No. NM_003194 (SEQ ID NO:441)), TATA box Forward primer
(SEQ ID NO:442): CGGTTTGCTGCGGTAATCAT TATA box Reverse primer (SEQ
ID NO:443): TTTCTTGCTGCCAGTCTGGAC TATA box-amplicon (SEQ ID
NO:444): CGGTTTGCTGCGGTAATCATGAGGATAAGAGAGCCACGAACCACGGCACTG
ATTTTCAGTTCTGGGAAAATGGTGTGCACAGGAGCCAAGAGTGAAGAACAGTCCAGACTGGCAGCAAGAAA
Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:445))
Ubiquitin Forward primer (SEQ ID NO:446): ATTTGGGTCGCGGTTCTTG
Ubiquitin Reverse primer (SEQ ID NO:447): TGCCTTGACATTCTCGATGGT
Ubiquitin-amplicon (SEQ ID NO:448):
ATTTGGGTCGCGGTTCTTGTTTGTGGATCGCTGTGATCGTCACTTGACAA
TGCAGATCTTCGTGAAGACTCTGACTGGTAAGACCATCACCCTCGAGGTTGAGCCCAGTGACACCATCGAGAAT-
GTCAAGGCA SDHA (GenBank Accession No. NM_004168 (SEQ ID NO:449))
SDHA Forward primer (SEQ ID NO:450): TGGGAACAAGAGGGCATCTG SDHA
Reverse primer (SEQ ID NO:451): CCACCACTGCATCAAATTCATG
SDHA-amplicon (SEQ ID NO:452):
TGGGAACAAGAGGGCATCTGCTAAAGTTTCAGATTCCATTTCTGCTCAGTATCCA
GTAGTGGATCATGAATTTGATGCAGTGGTGG
Description for Cluster S67314
Cluster S67314 features 4 transcript(s) and 8 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00006 TABLE 1 Transcripts of interest Transcript Name SEQ
ID NO S67314_PEA_1_T4 1 S67314_PEA_1_T5 2 S67314_PEA_1_T6 3
S67314_PEA_1_T7 4
TABLE-US-00007 TABLE 2 Segments of interest Segment Name SEQ ID NO
S67314_PEA_1_node_0 65 S67314_PEA_1_node_11 66 S67314_PEA_1_node_13
67 S67314_PEA_1_node_15 68 S67314_PEA_1_node_17 69
S67314_PEA_1_node_4 70 S67314_PEA_1_node_10 71 S67314_PEA_1_node_3
72
TABLE-US-00008 TABLE 3 Proteins of interest Protein Name SEQ ID NO
S67314_PEA_1_P4 281 S67314_PEA_1_P5 282 S67314_PEA_1_P6 283
S67314_PEA_1_P7 284
These sequences are variants of the known protein Fatty
acid-binding protein, heart (SEQ ID NO:348) (SwissProt accession
identifier FABH_HUMAN; known also according to the synonyms H-FABP;
Muscle fatty acid-binding protein; M-FABP; Mammary-derived growth
inhibitor; MDGI), referred to herein as the previously known
protein.
Protein Fatty acid-binding protein, heart (SEQ ID NO:348) is known
or believed to have the following function(s): FABP are thought to
play a role in the intracellular transport of long-chain fatty
acids and their acyl-CoA esters. The sequence for protein Fatty
acid-binding protein, heart is given at the end of the application,
as "Fatty acid-binding protein, heart amino acid sequence" (SEQ ID
NO:348). Known polymorphisms for this sequence are as shown in
Table 4.
TABLE-US-00009 TABLE 4 Amino acid mutations for Known Protein SNP
position(s) on amino acid sequence Comment 1 V -> A 104 L ->
K 124 C -> S 129 E -> Q
Protein Fatty acid-binding protein, heart (SEQ ID NO:348)
localization is believed to be Cytoplasmic.
The following GO Annotation(s) apply to the previously known
protein. The following annotation(s) were found: negative control
of cell proliferation, which are annotation(s) related to
Biological Process; and lipid binding, which are annotation(s)
related to Molecular Function.
The GO assignment relies on information from one or more of the
SwissProt/TremB1 Protein knowledgebase, available from <dot
expasy dot ch/sprot/>; or Locuslink, available from <dot ncbi
dot nlm dot nih dot gov/projects/LocusLink/>.
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster S67314. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 2 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 2, concerning the number of heart-specific
clones in libraries/sequences; as well as with regard to the
histogram in FIGS. 3-4, concerning the actual expression of
oligonucleotides in various tissues, including heart.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs, which was found to be 13.8; the ratio of
expression of the cluster in heart specific ESTs to the overall
expression of the cluster in muscle-specific ESTs which was found
to be 2.6; and fisher exact test P-values were computed both for
library and weighted clone counts to check that the counts are
statistically significant, and were found to be 1.10E-25.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the ratio of expression of the cluster
in heart specific ESTs to the overall expression of the cluster in
muscle-specific ESTs which was found to be 2.6, which clearly
supports specific expression in heart tissue.
As noted above, cluster S67314 features 4 transcript(s), which were
listed in Table 1 above. These transcript(s) encode for protein(s)
which are variant(s) of protein Fatty acid-binding protein, heart
(SEQ ID NO:348). A description of each variant protein according to
the present invention is now provided.
Variant protein S67314_PEA.sub.--1_P4 (SEQ ID NO:281) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
S67314_PEA.sub.--1_T4 (SEQ ID NO:1). An alignment is given to the
known protein (Fatty acid-binding protein, heart (SEQ ID NO:348))
at the end of the application. One or more alignments to one or
more previously published protein sequences are given at the end of
the application. A brief description of the relationship of the
variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between S67314_PEA.sub.--1_P4 (SEQ ID NO:281) and
FABH_HUMAN (SEQ ID NO:348):
1. An isolated chimeric polypeptide encoding for
S67314_PEA.sub.--1_P4 (SEQ ID NO:281), comprising a first amino
acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence MVDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTF
KNTEISFKLGVEFDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLIL
corresponding to amino acids 1-116 of FABH_HUMAN (SEQ ID NO:348),
which also corresponds to amino acids 1-116 of
S67314_PEA.sub.--1_P4 (SEQ ID NO:281), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
VRWATLELYLIGYYYCSFSQACSKKPSPPLRAVEAGTREWLWVRVVSGGNFLCSGFGL
TQAGTQILPYRLHDCGQITFSKCNCKTGINNTNLVGLLGSL (SEQ ID NO:396)
corresponding to amino acids 117-215 of S67314_PEA.sub.--1_P4 (SEQ
ID NO:281), wherein said first and second amino acid sequences are
contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
S67314_PEA.sub.--1_P4 (SEQ ID NO:281), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VRWATLELYLIGYYYCSFSQACSKKPSPPLRAVEAGTREWLWVRVVSGGNFLCSGFGL
TQAGTQILPYRLHDCGQITFSKCNCKTGINNTNLVGLLGSL (SEQ ID NO:396) in
S67314_PEA.sub.--1_P4 (SEQ ID NO:281).
Comparison report between S67314_PEA.sub.--1_P4 (SEQ ID NO:281) and
AAP35373 (SEQ ID NO:348):
1. An isolated chimeric polypeptide encoding for
S67314_PEA.sub.--1_P4 (SEQ ID NO:281), comprising a first amino
acid sequence being at least 90% homologous to
MVDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTF
KNTEISFKLGVEFDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLIL
corresponding to amino acids 1-116 of AAP35373 (SEQ ID NO:348),
which also corresponds to amino acids 1-116 of
S67314_PEA.sub.--1_P4 (SEQ ID NO:281), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
VRWATLELYLIGYYYCSFSQACSKKPSPPLRAVEAGTREWLWVRVVSGGNFLCSGFGL
TQAGTQILPYRLHDCGQITFSKCNCKTGINNTNLVGLLGSL (SEQ ID NO:396)
corresponding to amino acids 117-215 of S67314_PEA.sub.--1_P4 (SEQ
ID NO:281), wherein said first and second amino acid sequences are
contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
S67314_PEA.sub.--1_P4 (SEQ ID NO:281), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VRWATLELYLIGYYYCSFSQACSKKPSPPLRAVEAGTREWLWVRVVSGGNFLCSGFGL
TQAGTQILPYRLHDCGQITFSKCNCKTGINNTNLVGLLGSL (SEQ ID NO:396) in
S67314_PEA.sub.--1_P4 (SEQ ID NO:281).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein S67314_PEA.sub.--1_P4 (SEQ ID NO:281) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 5, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein S67314_PEA.sub.--1_P4 (SEQ ID
NO:281) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00010 TABLE 5 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
53 K -> R Yes
Variant protein S67314_PEA.sub.--1_P4 (SEQ ID NO:281) is encoded by
the following transcript(s): S67314_PEA.sub.--1_T4 (SEQ ID NO:1),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript S67314_PEA.sub.--1_T4
(SEQ ID NO:1) is shown in bold; this coding portion starts at
position 925 and ends at position 1569. The transcript also has the
following SNPs as listed in Table 6 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
S67314_PEA.sub.--1.sub.--P4 (SEQ ID NO:281) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00011 TABLE 6 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
580 T -> C Yes 1082 A -> G Yes 1670 A -> C Yes
Variant protein S67314_PEA.sub.--1_P5 (SEQ ID NO:282) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s) S67314_PEA
1_T5 (SEQ ID NO:2). An alignment is given to the known protein
(Fatty acid-binding protein, heart (SEQ ID NO:348)) at the end of
the application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between S67314_PEA.sub.--1_P5 (SEQ ID NO:282) and
FABH_HUMAN (SEQ ID NO:348):
1. An isolated chimeric polypeptide encoding for
S67314_PEA.sub.--1_P5 (SEQ ID NO:282), comprising a first amino
acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence MVDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTF
KNTEISFKLGVEFDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLIL
corresponding to amino acids 1-116 of FABH_HUMAN (SEQ ID NO:348),
which also corresponds to amino acids 1-116 of
S67314_PEA.sub.--1_P5 (SEQ ID NO:282), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
DVLTAWPSIYRRQVKVLREDEITILPWHLQWSREKATKLLRPTLPSYNNHGWEELRVG KSIV
(SEQ ID NO:397) corresponding to amino acids 117-178 of
S67314_PEA.sub.--1_P5 (SEQ ID NO:282), wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
S67314_PEA.sub.--1_P5 (SEQ ID NO:282), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
DVLTAWPSIYRRQVKVLREDEITILPWHLQWSREKATKLLRPTLPSYNNHGWEELRVG KSIV
(SEQ ID NO:397) in S67314_PEA.sub.--1_P5 (SEQ ID NO:282).
Comparison report between S67314_PEA.sub.--1_P5 (SEQ ID NO:282) and
AAP35373 (SEQ ID NO:348):
1. An isolated chimeric polypeptide encoding for
S67314_PEA.sub.--1_P5 (SEQ ID NO:282), comprising a first amino
acid sequence being at least 90% homologous to
MVDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTF
KNTEISFKLGVEFDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLIL
corresponding to amino acids 1-116 of AAP35373 (SEQ ID NO:348),
which also corresponds to amino acids 1-116 of
S67314_PEA.sub.--1_P5 (SEQ ID NO:282), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
DVLTAWPSIYRRQVKVLREDEITILPWHLQWSREKATKLLRPTLPSYNNHGWEELRVG KSIV
(SEQ ID NO:397) corresponding to amino acids 117-178 of
S67314_PEA.sub.--1_P5 (SEQ ID NO:282), wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
S67314_PEA.sub.--1_P5 (SEQ ID NO:282), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
DVLTAWPSIYRRQVKVLREDEITILPWHLQWSREKATKLLRPTLPSYNNHGWEELRVG KSIV
(SEQ ID NO:397) in S67314_PEA.sub.--1_P5 (SEQ ID NO:282).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein S67314_PEA.sub.--1_P5 (SEQ ID NO:282) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 7, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein S67314_PEA.sub.--1_P5 (SEQ ID
NO:282) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00012 TABLE 7 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
53 K -> R Yes
Variant protein S67314_PEA.sub.--1_P5 (SEQ ID NO:282) is encoded by
the following transcript(s): S67314_PEA.sub.--1_T5 (SEQ ID NO:2),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript S67314_PEA.sub.--1_T5
(SEQ ID NO:2) is shown in bold; this coding portion starts at
position 925 and ends at position 1458. The transcript also has the
following SNPs as listed in Table 8 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
S67314_PEA.sub.--1_P5 (SEQ ID NO:282) sequence provides support for
the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00013 TABLE 8 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
580 T -> C Yes 1082 A -> G Yes 1326 A -> G Yes
Variant protein S67314_PEA.sub.--1_P6 (SEQ ID NO:283) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
S67314_PEA.sub.--1_T6 (SEQ ID NO:3). An alignment is given to the
known protein (Fatty acid-binding protein, heart (SEQ ID NO:348))
at the end of the application. One or more alignments to one or
more previously published protein sequences are given at the end of
the application. A brief description of the relationship of the
variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between S67314_PEA.sub.--1_P6 (SEQ ID NO:283) and
FABH_HUMAN (SEQ ID NO:348):
1. An isolated chimeric polypeptide encoding for
S67314_PEA.sub.--1_P6 (SEQ ID NO:283), comprising a first amino
acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence MVDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTF
KNTEISFKLGVEFDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLIL
corresponding to amino acids 1-116 of FABH_HUMAN (SEQ ID NO:348),
which also corresponds to amino acids 1-116 of
S67314_PEA.sub.--1_P6 (SEQ ID NO:283), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
MEKLQLRNVK (SEQ ID NO:398) corresponding to amino acids 117-126 of
S67314_PEA.sub.--1_P6 (SEQ ID NO:283), wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
S67314_PEA.sub.--1_P6 (SEQ ID NO:283), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence MEKLQLRNVK
(SEQ ID NO:398) in S67314_PEA.sub.--1_P6 (SEQ ID NO:283).
Comparison report between S67314_PEA.sub.--1_P6 (SEQ ID NO:283) and
AAP35373 (SEQ ID NO:348):
1. An isolated chimeric polypeptide encoding for
S67314_PEA.sub.--1_P6 (SEQ ID NO:283), comprising a first amino
acid sequence being at least 90% homologous to
MVDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTF
KNTEISFKLGVEFDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLIL
corresponding to amino acids 1-116 of AAP35373 (SEQ ID NO:348),
which also corresponds to amino acids 1-116 of
S67314_PEA.sub.--1_P6 (SEQ ID NO:283), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
MEKLQLRNVK (SEQ ID NO:398) corresponding to amino acids 117-126 of
S67314_PEA.sub.--1_P6 (SEQ ID NO:283), wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
S67314_PEA.sub.--1_P6 (SEQ ID NO:283), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence MEKLQLRNVK
(SEQ ID NO:398) in S67314_PEA.sub.--1_P6 (SEQ ID NO:283).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein S67314_PEA.sub.--1_P6 (SEQ ID NO:283) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 9, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein S67314_PEA.sub.--1_P6 (SEQ ID
NO:283) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00014 TABLE 9 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
53 K -> R Yes
Variant protein S67314_PEA.sub.--1_P6 (SEQ ID NO:283) is encoded by
the following transcript(s): S67314_PEA.sub.--1_T6 (SEQ ID NO:3),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript S67314_PEA.sub.--1_T6
(SEQ ID NO:3) is shown in bold; this coding portion starts at
position 925 and ends at position 1302. The transcript also has the
following SNPs as listed in Table 10 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
S67314_PEA.sub.--1_P6 (SEQ ID NO:283) sequence provides support for
the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00015 TABLE 10 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
580 T -> C Yes 1082 A -> G Yes 1444 T -> C Yes
Variant protein S67314_PEA.sub.--1_P7 (SEQ ID NO:284) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
S67314_PEA.sub.--1_T7 (SEQ ID NO:4). An alignment is given to the
known protein (Fatty acid-binding protein, heart (SEQ ID NO:348))
at the end of the application. One or more alignments to one or
more previously published protein sequences are given at the end of
the application. A brief description of the relationship of the
variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between S67314_PEA.sub.--1_P7 (SEQ ID NO:284) and
FABH_HUMAN (SEQ ID NO:348):
1. An isolated chimeric polypeptide encoding for
S67314_PEA.sub.--1_P7 (SEQ ID NO:284), comprising a first amino
acid sequence being at least 90% homologous to
MVDAFLGTWKLVDSKNFDDYMKSL corresponding to amino acids 1-24 of
FABH_HUMAN (SEQ ID NO:348), which also corresponds to amino acids
1-24 of S67314_PEA.sub.--1_P7 (SEQ ID NO:284), second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
AHILITFPLPS (SEQ ID NO:399) corresponding to amino acids 25-35 of
S67314_PEA.sub.--1_P7 (SEQ ID NO:284), and a third amino acid
sequence being at least 90% homologous to
GVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNTEISFKLGVEFDETTADDRKVKSI
VTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHGTAVCTRTYEKEA corresponding to
amino acids 25-133 of FABH_HUMAN (SEQ ID NO:348), which also
corresponds to amino acids 36-144 of S67314_PEA.sub.--1_P7 (SEQ ID
NO:284), wherein said first, second, third and fourth amino acid
sequences are contiguous and in a sequential order.
2. An isolated polypeptide encoding for an edge portion of
S67314_PEA.sub.--1_P7 (SEQ ID NO:284), comprising an amino acid
sequence being at least 70%, optionally at least about 80%,
preferably at least about 85%, more preferably at least about 90%
and most preferably at least about 95% homologous to the sequence
encoding for AHILITFPLPS (SEQ ID NO:399), corresponding to
S67314_PEA.sub.--1_P7 (SEQ ID NO:284).
Comparison report between S67314_PEA.sub.--1_P7 (SEQ ID NO:284) and
AAP35373 (SEQ ID NO:348):
1. An isolated chimeric polypeptide encoding for
S67314_PEA.sub.--1_P7 (SEQ ID NO:284), comprising a first amino
acid sequence being at least 90% homologous to
MVDAFLGTWKLVDSKNFDDYMKSL corresponding to amino acids 1-24 of
AAP35373 (SEQ ID NO:348), which also corresponds to amino acids
1-24 of S67314_PEA.sub.--1_P7 (SEQ ID NO:284), second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
AHILITFPLPS (SEQ ID NO:399) corresponding to amino acids 25-35 of
S67314_PEA.sub.--1_P7 (SEQ ID NO:284), and a third amino acid
sequence being at least 90% homologous to
GVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNTEISFKLGVEFDETTADDRKVKSI
VTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHGTAVCTRTYEKEA corresponding to
amino acids 25-133 of AAP35373 (SEQ ID NO:348), which also
corresponds to amino acids 36-144 of S67314_PEA.sub.--1_P7 (SEQ ID
NO:284), wherein said first, second and third amino acid sequences
are contiguous and in a sequential order.
2. An isolated polypeptide encoding for an edge portion of
S67314_PEA.sub.--1_P7 (SEQ ID NO:284), comprising an amino acid
sequence being at least 70%, optionally at least about 80%,
preferably at least about 85%, more preferably at least about 90%
and most preferably at least about 95% homologous to the sequence
encoding for AHILITFPLPS (SEQ ID NO:399), corresponding to
S67314_PEA.sub.--1_P7 (SEQ ID NO:284).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein S67314_PEA.sub.--1_P7 (SEQ ID NO:284) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 11, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein S67314_PEA.sub.--1_P7 (SEQ ID
NO:284) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00016 TABLE 11 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
64 K -> R Yes
Variant protein S67314_PEA.sub.--1_P7 (SEQ ID NO:284) is encoded by
the following transcript(s): S67314_PEA.sub.--1_T7 (SEQ ID NO:4),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript S67314_PEA.sub.--1_T7
(SEQ ID NO:4) is shown in bold; this coding portion starts at
position 925 and ends at position 1356. The transcript also has the
following SNPs as listed in Table 12 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
S67314_PEA.sub.--1_P7 (SEQ ID NO:284) sequence provides support for
the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00017 TABLE 12 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
580 T -> C Yes 1115 A -> G Yes 2772 G -> A Yes 2896 C
-> A Yes 2918 G -> C Yes 3003 A -> G Yes 3074 T -> G
Yes 1344 T -> C Yes 1522 -> T No 1540 -> A No 1540 -> T
No 1578 G -> A Yes 1652 G -> A Yes 2263 G -> A Yes 2605 T
-> C Yes
As noted above, cluster S67314 features 8 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster S67314_PEA.sub.--1_node.sub.--0 (SEQ ID NO:65)
according to the present invention is supported by 90 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
S67314_PEA.sub.--1_T4 (SEQ ID NO:1), S67314_PEA.sub.--1_T5 (SEQ ID
NO:2), S67314_PEA.sub.--1_T6 (SEQ ID NO:3) and
S67314_PEA.sub.--1_T7 (SEQ ID NO:4). Table 13 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00018 TABLE 13 Segment location on transcripts Segment
Segment Transcript name starting position ending position
S67314_PEA_1_T4 (SEQ ID 1 997 NO: 1) S67314_PEA_1_T5 (SEQ ID 1 997
NO: 2) S67314_PEA_1_T6 (SEQ ID 1 997 NO: 3) S67314_PEA_1_T7 (SEQ ID
1 997 NO: 4)
Segment cluster S67314_PEA.sub.--1_node.sub.--11 (SEQ ID NO:66)
according to the present invention is supported by 6 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
S67314_PEA.sub.--1_T4 (SEQ ID NO:1). Table 14 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00019 TABLE 14 Segment location on transcripts Segment
Segment Transcript name starting position ending position
S67314_PEA_1_T4 (SEQ ID 1273 2110 NO: 1)
Segment cluster S67314_PEA.sub.--1_node.sub.--13 (SEQ ID NO:67)
according to the present invention is supported by 76 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
S67314_PEA.sub.--1_T7 (SEQ ID NO:4). Table 15 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00020 TABLE 15 Segment location on transcripts Segment
Segment Transcript name starting position ending position
S67314_PEA_1_T7 (SEQ ID 1306 3531 NO: 4)
Segment cluster S67314_PEA.sub.--1_node.sub.--15 (SEQ ID NO:68)
according to the present invention is supported by 1 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
S67314_PEA.sub.--1_T5 (SEQ ID NO:2). Table 16 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00021 TABLE 16 Segment location on transcripts Segment
Segment Transcript name starting position ending position
S67314_PEA_1_T5 (SEQ ID 1273 1733 NO: 2)
Segment cluster S67314_PEA.sub.--1_node.sub.--17 (SEQ ID NO:69)
according to the present invention is supported by 4 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
S67314_PEA.sub.--1_T6 (SEQ ID NO:3). Table 17 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00022 TABLE 17 Segment location on transcripts Segment
Segment Transcript name starting position ending position
S67314_PEA_1_T6 (SEQ ID 1273 1822 NO: 3)
Segment cluster S67314_PEA.sub.--1_node.sub.--4 (SEQ ID NO:70)
according to the present invention is supported by 101 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
S67314_PEA.sub.--1_T4 (SEQ ID NO:1), S67314_PEA.sub.--1_T5 (SEQ ID
NO:2), S67314_PEA.sub.--1_T6 (SEQ ID NO:3) and
S67314_PEA.sub.--1_T7 (SEQ ID NO:4). Table 19 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00023 TABLE 19 Segment location on transcripts Segment
Segment Transcript name starting position ending position
S67314_PEA_1_T4 (SEQ ID 998 1170 NO: 1) S67314_PEA_1_T5 (SEQ ID 998
1170 NO: 2) S67314_PEA_1_T6 (SEQ ID 998 1170 NO: 3) S67314_PEA_1_T7
(SEQ ID 1031 1203 NO: 4)
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster S67314_PEA.sub.--1_node.sub.--10 (SEQ ID NO:71)
according to the present invention is supported by 64 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
S67314_PEA.sub.--1_T4 (SEQ ID NO:1), S67314_PEA.sub.--1_T5 (SEQ ID
NO:2), S67314_PEA.sub.--1_T6 (SEQ ID NO:3) and
S67314_PEA.sub.--1_T7 (SEQ ID NO:4). Table 20 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00024 TABLE 20 Segment location on transcripts Segment
Segment Transcript name starting position ending position
S67314_PEA_1_T4 (SEQ ID 1171 1272 NO: 1) S67314_PEA_1_T5 (SEQ ID
1171 1272 NO: 2) S67314_PEA_1_T6 (SEQ ID 1171 1272 NO: 3)
S67314_PEA_1_T7 (SEQ ID 1204 1305 NO: 4)
Segment cluster S67314_PEA.sub.--1_node.sub.--3 (SEQ ID NO:72)
according to the present invention is supported by 1 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
S67314_PEA.sub.--1_T7 (SEQ ID NO:4). Table 21 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00025 TABLE 21 Segment location on transcripts Segment
Segment Transcript name starting position ending position
S67314_PEA_1_T7 (SEQ ID 998 1030 NO: 4)
Variant protein alignment to the previously known protein: Sequence
name: /tmp/EQ0nMn6tqU/R73CUVKUk5:FABH_HUMAN (SEQ ID NO:348)
Sequence documentation: Alignment of: S67314_PEA.sub.--1_P4 (SEQ ID
NO:281) x FABH_HUMAN (SEQ ID NO:348)
TABLE-US-00026 Alignment segment 1/1: Quality: 1095.00 Escore: 0
Matching length: 115 Total length: 115 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00001## Sequence name: /tmp/EQ0nMn6tqU/R73CUVKUk5:AAP35373
(SEQ ID NO:348) Sequence documentation: Alignment of:
S67314_PEA.sub.--1_P4 (SEQ ID NO:281) x AAP35373 (SEQ ID
NO:348).
TABLE-US-00027 Alignment segment 1/1: Quality: 1107.00 Escore: 0
Matching length: 116 Total length: 116 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00002## Sequence name: /tmp/ql4YPIBbdQ/SeofJfCmJW:FABH_HUMAN
(SEQ ID NO:348) Sequence documentation: Alignment of:
S67314_PEA.sub.--1_P5 (SEQ ID NO:282) x FABH_HUMAN (SEQ ID
NO:348).
TABLE-US-00028 Alignment segment 1/1: Quality: 1095.00 Escore: 0
Matching length: 115 Total length: 115 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00003## Sequence name: /tmp/ql4YPIBbdQ/SeofJfCmJW:AAP35373
(SEQ ID NO:348) Sequence documentation: Alignment of:
S67314_PEA.sub.--1_P5 (SEQ ID NO:282) x AAP35373 (SEQ ID
NO:348).
TABLE-US-00029 Alignment segment 1/1: Quality: 1107.00 Escore: 0
Matching length: 116 Total length: 116 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00004## Sequence name:/tmp/PXra2DxL1v/Q8GTrzNMVX:FABH_HUMAN
(SEQ ID NO:348) Sequence documentation: Alignment of:
S67314_PEA.sub.--1_P6 (SEQ ID NO:283) x FABH_HUMAN (SEQ ID
NO:348).
TABLE-US-00030 Alignment segment 1/1: Quality: 1095.00 Escore: 0
Matching length: 115 Total length: 115 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00005## Sequence name: /tmp/PXra2DxL1v/Q8GTrzNMVX:AAP35373
(SEQ ID NO:348) Sequence documentation: Alignment of:
S67314_PEA.sub.--1_P6 (SEQ ID NO:283) x AAP35373 (SEQ ID
NO:348).
TABLE-US-00031 Alignment segment 1/1: Quality: 1107.00 Escore: 0
Matching length: 116 Total length: 116 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00006## Sequence name: /tmp/xYzWyViDom/twDu3T69pd:FABH_HUMAN
(SEQ ID NO:348) Sequence documentation: Alignment of:
S67314_PEA.sub.--1_P7 (SEQ ID NO:284) x FABH_HUMAN (SEQ ID
NO:348).
TABLE-US-00032 Alignment segment 1/1: Quality: 1160.00 Escore: 0
Matching length: 132 Total length: 143 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
92.31 Total Percent Identity: 92.31 Gaps: 1
Alignment:
##STR00007## Sequence name: /tmp/xYzWyViDom/twDu3T69pd:AAP35373
(SEQ ID NO:348) Sequence documentation: Alignment of:
S67314_PEA.sub.--1_P7 (SEQ ID NO:284) x AAP35373 (SEQ ID
NO:348).
TABLE-US-00033 Alignment segment 1/1: Quality: 1172.00 Escore: 0
Matching length: 133 Total length: 144 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
92.36 Total Percent Identity: 92.36 Gaps: 1
Alignment:
##STR00008## Expression of FABH_HUMAN Fatty acid-binding protein
transcripts which are detectable by amplicon as depicted in
sequence name S67314 specifically in heart tissue.
Expression of FABH_HUMAN Fatty acid-binding protein transcripts
detectable by or according to seg11, S67314 amplicon(s) and S67314
seg11F (SEQ ID NO:61) and S67314 seg11R (SEQ ID NO:62) primers was
measured by real time PCR. In parallel the expression of four
housekeeping genes--RPL19 (GenBank Accession No. NM.sub.--000981
(SEQ ID NO:437); RPL19 amplicon (SEQ ID NO:440)), TATA box (GenBank
Accession No. NM.sub.--003194 (SEQ ID NO:441); TATA amplicon (SEQ
ID NO:444)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID
NO:445); amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA
(GenBank Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)) was measured similarly.
For each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the median of the quantities of the heart samples
(Sample Nos. 44, 45, 46, Table 1, "Tissue samples in testing
panel", above), to obtain a value of fold up-regulation for each
sample relative to median of the heart.
FIG. 5A is a histogram showing specific expression of the
above-indicated FABH_HUMAN Fatty acid-binding protein transcripts
in heart tissue samples as opposed to other tissues.
As is evident from FIG. 5A, the expression of FABH_HUMAN Fatty
acid-binding protein transcripts detectable by the above
amplicon(s) in heart tissue samples was significantly higher than
in most other samples (non heart tissue sample Nos. 1-11, 13-21,
23-26, 28-43, 47-74, Table 1 above, "Tissue samples in testing
panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: S67314 seg11F (SEQ ID
NO:61) forward primer; and S67314 seg11R (SEQ ID NO:62) reverse
primer.
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
S67314 seg11 (SEQ ID NO:63).
TABLE-US-00034 S67314 seg11F (SEQ ID NO:61): TCCCCTGAGAGCTGTAGAA
GCT S67314 seg11R (SEQ ID NO:62): CGGCCTGTGTGAGTCCAAA S67314 seg11
(SEQ ID NO:63): TCCCCTGAGAGCTGTAGAAGC
TGGGACAAGAGAGTGGTTGTGGGTCAGGGTGGTATCAGGTGGGAATTTTC
TGTGTAGTGGCTTTGGACTCACACAGGCCG
Expression of FABH_HUMAN Fatty acid-binding protein S67314
transcripts, which are detectable by amplicon as depicted in
sequence name S67314 seg15 specifically in heart tissue
Expression of FABH_HUMAN Fatty acid-binding protein transcripts
detectable by or according to seg15 node(s), S67314 seg15
amplicon(s) and S67314 seg15F and S67314 seg15R primers was
measured by real time PCR. In parallel the expression of four
housekeeping genes--RPL19 (GenBank Accession No. NM.sub.--000981
(SEQ ID NO:437); RPL19 amplicon (SEQ ID NO:440)), TATA box (GenBank
Accession No. NM.sub.--003194 (SEQ ID NO:441); TATA amplicon (SEQ
ID NO:444)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID
NO:445); amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA
(GenBank Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)), was measured similarly.
For each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the median of the quantities of the heart samples
(Sample Nos. 44-46, Table 1, above "Tissue samples in testing
panel"), to obtain a value of fold up-regulation for each sample
relative to median of the heart.
FIG. 5B is a histogram showing specific expression of the
above-indicated FABH_HUMAN Fatty acid-binding protein transcripts
in heart tissue samples as opposed to other tissues.
As is evident from FIG. 5B, the expression of FABH_HUMAN Fatty
acid-binding protein transcripts detectable by the above
amplicon(s) in heart tissue samples was significantly higher than
in most other samples (non-heart tissue sample Nos. 1-9, 11-21,
23-26, 28-43, 47-74 Table 1 above, "Tissue samples in testing
panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: S67314 seg15F Forward
primer (SEQ ID NO:64); and S67314 seg15R Reverse primer (SEQ ID
NO:274).
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
S67314 seg15.
TABLE-US-00035 S67314 seg15F (SEQ ID NO:64) Forward primer:
TTCCTTGGCATCTCCAATGG S67314 seg15R (SEQ ID NO:274) Reverse primer:
GCCAACTCTCAGCTCCTCCC S67314 seg15 (SEQ ID NO:275) Amplicon:
TTCCTTGGCATCTCCAATGGAGTAGAGAGAAGGCAACAAAGCTTCTCAG
ACCCACATTACCGAGCTATAACAACCATGGCTGGGAGGAGCTGAGAGTT GGC
Expression of FABH_HUMAN Fatty acid-binding protein S67314
transcripts which are detectable by amplicon as depicted in
sequence name S67314seg4 specifically in heart tissue
Expression of FABH_HUMAN Fatty acid-binding protein transcripts
detectable by or according to seg4 node(s), S67314 seg4 amplicon(s)
and primers S67314seg4F and S67314seg4R was measured by real time
PCR (this transcript corresponds to the known or WT protein). In
parallel the expression of four housekeeping genes--RPL19 (GenBank
Accession No. NM.sub.--000981 (SEQ ID NO:437); RPL19 amplicon (SEQ
ID NO:440)), TATA box (GenBank Accession No. NM.sub.--003194 (SEQ
ID NO:441); TATA amplicon (SEQ ID NO:444)), Ubiquitin (GenBank
Accession No. BC000449 (SEQ ID NO:445);
amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA (GenBank
Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)), was measured similarly.
For each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the median of the quantities of the heart samples
(Sample Nos. 44-46, Table 1, above), to obtain a value of relative
expression for each sample relative to median of the heart
samples.
FIG. 6 is a histogram showing relative expression of the
above-indicated FABH_HUMAN Fatty acid-binding protein transcripts
in heart tissue samples as opposed to other tissues.
As is evident from FIG. 6, the expression of FABH_HUMAN Fatty
acid-binding protein transcripts detectable by the above
amplicon(s) in heart tissue samples was significantly higher than
in the other samples (Sample Nos. 44-46 Table 1, "Tissue samples in
testing panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: S67314seg4F forward primer
(SEQ ID NO:276); and S67314seg4R reverse primer (SEQ ID
NO:277).
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
S67314seg4.
TABLE-US-00036 Forward primer S67314seg4F (SEQ ID NO:276):
CCAAGCCTACCACAATCATCG Reverse primer S67314seg4R (SEQ ID NO:277):
CTCCACCCCCAACTTAAAGCT Amplicon S67314seg4 (SEQ ID NO:278):
CCAAGCCTACCACAATCATCGAAAAGAATGGGGACATTCTCACCCTAAAA
ACACACAGCACCTTCAAGAACACAGAGATCAGCTTTAAGTTGGGGGTGG AG
Description for Cluster N56180
Cluster N56180 features 7 transcript(s) and 22 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00037 TABLE 1 Transcripts of interest Transcript Name Seq
ID No. N56180_T1 5 N56180_T3 6 N56180_T4 7 N56180_T5 8 N56180_T6 9
N56180_T7 10 N56180_T8 11
TABLE-US-00038 TABLE 2 Segments of interest Segment Name Seq ID No.
N56180_node_2 73 N56180_node_20 74 N56180_node_22 75 N56180_node_28
76 N56180_node_34 77 N56180_node_36 78 N56180_node_4 79
N56180_node_6 80 N56180_node_0 81 N56180_node_10 82 N56180_node_12
83 N56180_node_14 84 N56180_node_16 85 N56180_node_18 86
N56180_node_24 87 N56180_node_26 88 N56180_node_29 89 N56180_node_3
90 N56180_node_31 91 N56180_node_33 92 N56180_node_35 93
N56180_node_8 94
TABLE-US-00039 TABLE 3 Proteins of interest Protein Name Seq ID No.
N56180_P2 285 N56180_P4 286 N56180_P5 287 N56180_P6 288 N56180_P7
289 N56180_P8 290 N56180_P9 291
These sequences are variants of the known protein Calsequestrin,
cardiac muscle isoform precursor (SEQ ID NO:349) (SwissProt
accession identifier CAQ2_HUMAN; known also according to the
synonyms Calsequestrin 2), referred to herein as the previously
known protein.
Protein Calsequestrin, cardiac muscle isoform precursor (SEQ ID
NO:349) is known or believed to have the following function(s):
Calsequestrin is a high-capacity, moderate affinity,
calcium-binding protein and thus acts as an internal calcium store
in muscle. The release of calcium bound to calsequestrin through a
calcium release channel triggers muscle contraction. The protein
binds 40 to 50 moles of calcium. The sequence for protein
Calsequestrin, cardiac muscle isoform precursor is given at the end
of the application, as "Calsequestrin, cardiac muscle isoform
precursor amino acid sequence" (SEQ ID NO:349). Known polymorphisms
for this sequence are as shown in Table 4.
TABLE-US-00040 TABLE 4 Amino acid mutations for Known Protein SNP
position(s) on amino acid sequence Comment 307 D -> H (in
VTSIP). /FTId=VAR_016075. 67 Q -> P
Protein Calsequestrin, cardiac muscle isoform precursor (SEQ ID
NO:349) localization is believed to be in the sarcoplasmic
reticulum's terminal cisternae luminal spaces of cardiac and slow
skeletal muscle cells.
The following GO Annotation(s) apply to the previously known
protein. The following annotation(s) were found: striated muscle
contraction; heart development; muscle development, which are
annotation(s) related to Biological Process; calcium storage, which
are annotation(s) related to Molecular Function; and smooth
endoplasmic reticulum, which are annotation(s) related to Cellular
Component.
The GO assignment relies on information from one or more of the
SwissProt/TremB1 Protein knowledgebase, available from <dot
expasy dot ch/sprot/>; or Locuslink, available from <dot ncbi
dot nlm dot nih dot gov/projects/LocusLink/>.
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster N56180. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 7 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 7, concerning the number of heart-specific
clones in libraries/sequences; as well as with regard to the
histogram in FIG. 8, concerning the actual expression of
oligonucleotides in various tissues, including heart.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs was found to be 11; the ratio of
expression of the cluster in heart specific ESTs to the overall
expression of the cluster in muscle-specific ESTs was found to be
2.4; and fisher exact test P-values were computed both for library
and weighted clone counts to check that the counts are
statistically significant, and were found to be 4.70E-14.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the ratio of expression of the cluster
in heart specific ESTs to the overall expression of the cluster in
muscle-specific ESTs was found to be 2.4, which clearly supports
specific expression in heart tissue.
As noted above, cluster N56180 features 7 transcript(s), which were
listed in Table 1 above. These transcript(s) encode for protein(s)
which are variant(s) of protein Calsequestrin, cardiac muscle
isoform precursor (SEQ ID NO:349). A description of each variant
protein according to the present invention is now provided.
Variant protein N56180_P2 (SEQ ID NO:285) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) N56180_T1 (SEQ ID
NO:5). An alignment is given to the known protein (Calsequestrin,
cardiac muscle isoform precursor (SEQ ID NO:349)) at the end of the
application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between N56180_P2 (SEQ ID NO:285) and CAQ2_HUMAN
(SEQ ID NO:349):
1. An isolated chimeric polypeptide encoding for N56180_P2 (SEQ ID
NO:285), comprising a first amino acid sequence being at least 90%
homologous to
MKRTHLFIVGIYFLSSCRAEEGLNFPTYDGKDRVVSLSEKNFKQVLKKYDLLCLYYHEP
VSSDKVTQKQFQLKEIVLELVAQVLEHKAIGFVMVDAKKEAKLAKKLGFDEEGSLYIL
KGDRTIEFDGEFAADVLVEFLLDLIEDPVEIISSKLEVQAFERIEDYIKLIGFFKSEDSEYY
KAFEEAAEHFQPYIKFFATFDKGV corresponding to amino acids 1-203 of
CAQ2_HUMAN (SEQ ID NO:349), which also corresponds to amino acids
1-203 of N56180_P2 (SEQ ID NO:285), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
LWLTPVIPTLWEADGGGLHEPWSWRPAWATWLQRNYL (SEQ ID NO:400) corresponding
to amino acids 204-240 of N56180_P2 (SEQ ID NO:285), wherein said
first and second amino acid sequences are contiguous and in a
sequential order.
2. An isolated polypeptide encoding for a tail of N56180_P2 (SEQ ID
NO:285), comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence LWLTPVIPTLWEADGGGLHEPWSWRPAWATWLQRNYL (SEQ ID
NO:400) in N56180_P2 (SEQ ID NO:285).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted or localized in the sarcoplasmic reticulum's
terminal cisternae luminal spaces of cardiac and slow skeletal
muscle cells like the WT protein. The protein localization is
believed to be secreted because both signal-peptide prediction
programs predict that this protein has a signal peptide, and
neither trans-membrane region prediction program predicts that this
protein has a trans-membrane region.
Variant protein N56180_P2 (SEQ ID NO:285) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 7, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein N56180_P2 (SEQ ID NO:285) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00041 TABLE 7 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
66 T -> A Yes 76 V -> M Yes
Variant protein N56180_P2 (SEQ ID NO:285) is encoded by the
following transcript(s): N56180_T1 (SEQ ID NO:5), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript N56180_T1 (SEQ ID NO:5) is shown in bold;
this coding portion starts at position 242 and ends at position
961. The transcript also has the following SNPs as listed in Table
8 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein N56180_P2 (SEQ ID NO:285) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00042 TABLE 8 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
74 T -> No 105 T -> C Yes 2168 C -> G Yes 2289 G -> T
No 2489 A -> C No 2545 A -> Yes 2638 A -> T Yes 206 G
-> A Yes 221 G -> A Yes 228 A -> C Yes 437 A -> G Yes
467 G -> A Yes 1021 A -> No 1521 C -> T Yes 2018 C -> T
Yes
Variant protein N56180_P4 (SEQ ID NO:286) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) N56180_T3 (SEQ ID
NO:6). An alignment is given to the known protein (Calsequestrin,
cardiac muscle isoform precursor (SEQ ID NO:349)) at the end of the
application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between N56180_P4 (SEQ ID NO:286) and CAQ2_HUMAN
(SEQ ID NO:349):
1. An isolated chimeric polypeptide encoding for N56180_P4 (SEQ ID
NO:286), comprising a first amino acid sequence being at least 90%
homologous to
MKRTHLFIVGIYFLSSCRAEEGLNFPTYDGKDRVVSLSEKNFKQVLKKYDLLCLYYHEP
VSSDKVTQKQFQLKEIVLE corresponding to amino acids 1-78 of CAQ2_HUMAN
(SEQ ID NO:349), which also corresponds to amino acids 1-78 of
N56180_P4 (SEQ ID NO:286), second amino acid sequence being at
least 70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide having the sequence
HWQISQWWLHFQTPREEGKMKLLELSESADGAAWKRWGGNSNTHRIQ (SEQ ID NO:401)
corresponding to amino acids 79-125 of N56180_P4 (SEQ ID NO:286),
and a third amino acid sequence being at least 90% homologous to
LVAQVLEHKAIGFVMVDAKKEAKLAKKLGFDEEGSLYILKGDRTIEFDGEFAADVLVE
FLLDLIEDPVEIISSKLEVQAFERIEDYIKLIGFFKSEDSEYYKAFEEAAEHFQPYIKFFATF
DKGVAKKLSLKMNEVDFYEPFMDEPIAIPNKPYTEEELVEFVKEHQRPTLRRLRPEEMF
ETWEDDLNGIHIVAFAEKSDPDGYEFLEILKQVARDNTDNPDLSILWIDPDDFPLLVAY
WEKTFKIDLFRPQIGVVNVTDADSVWMEIPDDDDLPTAEELEDWIEDVLSGKINTEDDD
EDDDDDDNSDEEDNDDSDDDDDE corresponding to amino acids 79-399 of
CAQ2_HUMAN (SEQ ID NO:349), which also corresponds to amino acids
126-446 of N56180_P4 (SEQ ID NO:286), wherein said first, second
and third amino acid sequences are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for an edge portion of
N56180_P4 (SEQ ID NO:286), comprising an amino acid sequence being
at least 70%, optionally at least about 80%, preferably at least
about 85%, more preferably at least about 90% and most preferably
at least about 95% homologous to the sequence encoding for
HWQISQWWLHFQTPREEGKMKLLELSESADGAAWKRWGGNSNTHRIQ (SEQ ID NO:401),
corresponding to N56180_P4 (SEQ ID NO:286).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted or localized in the sarcoplasmic reticulum's
terminal cisternae luminal spaces of cardiac and slow skeletal
muscle cells like the WT protein. The protein localization is
believed to be secreted because both signal-peptide prediction
programs predict that this protein has a signal peptide, and
neither trans-membrane region prediction program predicts that this
protein has a trans-membrane region.
Variant protein N56180_P4 (SEQ ID NO:286) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 9, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein N56180_P4 (SEQ ID NO:286) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00043 TABLE 9 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
115 W -> R Yes 276 N -> No 66 T -> A Yes 76 .sup. V ->
M Yes
Variant protein N56180_P4 (SEQ ID NO:286) is encoded by the
following transcript(s): N56180_T3 (SEQ ID NO:6), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript N56180_T3 (SEQ ID NO:6) is shown in bold;
this coding portion starts at position 242 and ends at position
1579. The transcript also has the following SNPs as listed in Table
10 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein N56180_P4 (SEQ ID NO:286) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00044 TABLE 10 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
74 T -> No 105 T -> C Yes 2064 C -> T Yes 2214 C -> G
Yes 2335 G -> T No 2535 A -> C No 2591 A -> Yes 2684 A
-> T Yes 206 G -> A Yes 221 G -> A Yes 228 A -> C Yes
437 A -> G Yes 467 G -> A Yes 584 T -> C Yes 1067 A ->
No 1567 C -> T Yes
Variant protein N56180_P5 (SEQ ID NO:287) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) N56180_T4 (SEQ ID
NO:7). An alignment is given to the known protein (Calsequestrin,
cardiac muscle isoform precursor (SEQ ID NO:349)) at the end of the
application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between N56180_P5 (SEQ ID NO:287) and CAQ2_HUMAN
(SEQ ID NO:349):
1. An isolated chimeric polypeptide encoding for N56180_P5 (SEQ ID
NO:287), comprising a first amino acid sequence being at least 90%
homologous to
MKRTHLFIVGIYFLSSCRAEEGLNFPTYDGKDRVVSLSEKNFKQVLKKYDLLCLYYHEP
VSSDKVTQKQFQLKEIVLELVAQVLEHKAIGFVMVDAKKEAKLAKKLGFDEEGSLYIL
KGDRTIEFDGEFAADVLVEFLLD corresponding to amino acids 1-140 of
CAQ2_HUMAN (SEQ ID NO:349), which also corresponds to amino acids
1-140 of N56180_P5 (SEQ ID NO:287), and a second amino acid
sequence being at least 90% homologous to
VAKKLSLKMNEVDFYEPFMDEPIAIPNKPYTEEELVEFVKEHQRPTLRRLRPEEMFETW
EDDLNGIHIVAFAEKSDPDGYEFLEILKQVARDNTDNPDLSILWIDPDDFPLLVAYWEKT
FKIDLFRPQIGVVNVTDADSVWMEIPDDDDLPTAEELEDWIEDVLSGKINTEDDDEDDD
DDDNSDEEDNDDSDDDDDE corresponding to amino acids 203-399 of
CAQ2_HUMAN (SEQ ID NO:349), which also corresponds to amino acids
141-337 of N56180_P5 (SEQ ID NO:287), wherein said first and second
amino acid sequences are contiguous and in a sequential order.
2. An isolated chimeric polypeptide encoding for an edge portion of
N56180_P5 (SEQ ID NO:287), comprising a polypeptide having a length
"n", wherein "n" is at least about 10 amino acids in length,
optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least
about 40 amino acids in length and most preferably at least about
50 amino acids in length, wherein at least two amino acids comprise
DV, having a structure as follows: a sequence starting from any of
amino acid numbers 140-x to 140; and ending at any of amino acid
numbers 141+((n-2)-x), in which x varies from 0 to n-2.
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted or localized in the sarcoplasmic reticulum's
terminal cisternae luminal spaces of cardiac and slow skeletal
muscle cells like the WT protein. The protein localization is
believed to be secreted because both signal-peptide prediction
programs predict that this protein has a signal peptide, and
neither trans-membrane region prediction program predicts that this
protein has a trans-membrane region.
Variant protein N56180_P5 (SEQ ID NO:287) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 11, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein N56180_P5 (SEQ ID NO:287) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00045 TABLE 11 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
167 N -> No 66 T -> A Yes 76 .sup. V -> M Yes
Variant protein N56180_P5 (SEQ ID NO:287) is encoded by the
following transcript(s): N56180_T4 (SEQ ID NO:7), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript N56180_T4 (SEQ ID NO:7) is shown in bold;
this coding portion starts at position 242 and ends at position
1252. The transcript also has the following SNPs as listed in Table
12 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein N56180_P5 (SEQ ID NO:287) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00046 TABLE 12 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
74 T -> No 105 T -> C Yes 1887 C -> G Yes 2008 G -> T
No 2208 A -> C No 2264 A -> Yes 2357 A -> T Yes 206 G
-> A Yes 221 G -> A Yes 228 A -> C Yes 437 A -> G Yes
467 G -> A Yes 740 A -> No 1240 C -> T Yes 1737 C -> T
Yes
Variant protein N56180_P6 (SEQ ID NO:288) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) N56180_T5 (SEQ ID
NO:8). An alignment is given to the known protein (Calsequestrin,
cardiac muscle isoform precursor (SEQ ID NO:349)) at the end of the
application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between N56180.sub.13 P6 (SEQ ID NO:288) and
CAQ2_HUMAN (SEQ ID NO:349):
1. An isolated chimeric polypeptide encoding for N56180_P6 (SEQ ID
NO:288), comprising a
first amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence NETEAEQSYV (SEQ ID NO:402) corresponding to amino acids
1-10 of N56180_P6 (SEQ ID NO:288), second amino acid sequence being
at least 90% homologous to
RAEEGLNFPTYDGKDRVVSLSEKNFKQVLKKYDLLCLYYHEPVSSDKVTQKQFQLKEI
VLELVAQVLEHKAIGFVMVDAKKEAKLAKKL corresponding to amino acids 18-106
of CAQ2_HUMAN (SEQ ID NO:349), which also corresponds to amino
acids 11-99 of N56180_P6 (SEQ ID NO:288), a third (bridging) amino
acid sequence comprising D, and a fourth amino acid sequence being
at least 90% homologous to
YKAFEEAAEHFQPYIKFFATFDKGVAKKLSLKMNEVDFYEPFMDEPIAIPNKPYTEEEL
VEFVKEHQRPTLRRLRPEEMFETWEDDLNGIHIVAFAEKSDPDGYEFLEILKQVARDNT
DNPDLSILWIDPDDFPLLVAYWEKTFKIDLFRPQIGVVNVTDADSVWMEIPDDDDLPTA
EELEDWIEDVLSGKINTEDDDEDDDDDDNSDEEDNDDSDDDDDE corresponding to amino
acids 179-399 of CAQ2_HUMAN (SEQ ID NO:349), which also corresponds
to amino acids 101-321 of N56180_P6 (SEQ ID NO:288), wherein said
first, second, third and fourth amino acid sequences are contiguous
and in a sequential order.
2. An isolated polypeptide encoding for a head of N56180_P6 (SEQ ID
NO:288), comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence NETEAEQSYV (SEQ ID NO:402) of N56180_P6 (SEQ ID
NO:288).
3. An isolated polypeptide encoding for an edge portion of
N56180_P6 (SEQ ID NO:288), comprising a polypeptide having a length
"n", wherein "n" is at least about 10 amino acids in length,
optionally at least about 20 amino acids in length, preferably at
least about 30 amino acids in length, more preferably at least
about 40 amino acids in length and most preferably at least about
50 amino acids in length, wherein at least two amino acids comprise
LDY having a structure as follows (numbering according to N56180_P6
(SEQ ID NO:288)): a sequence starting from any of amino acid
numbers 99-x to 99; and ending at any of amino acid numbers
101+((n-2)-x), in which x varies from 0 to n-2.
Variant protein N56180_P6 (SEQ ID NO:288) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 13, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein N56180_P6 (SEQ ID NO:288) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00047 TABLE 13 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
151 N -> No 59 T -> A Yes 69 V -> M Yes
Variant protein N56180_P6 (SEQ ID NO:288) is encoded by the
following transcript(s): N56180_T5 (SEQ ID NO:8), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript N56180_T5 (SEQ ID NO:8) is shown in bold;
this coding portion starts at position 1 and ends at position 964.
The transcript also has the following SNPs as listed in Table 14
(given according to their position on the nucleotide sequence, with
the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein N56180_P6 (SEQ ID NO:288) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00048 TABLE 14 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
176 A -> G Yes 206 G -> A Yes 452 A -> No 952 C -> T
Yes 1449 C -> T Yes 1599 C -> G Yes 1720 G -> T No 1920 A
-> C No 1976 A -> Yes 2069 A -> T Yes
Variant protein N56180_P7 (SEQ ID NO:289) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) N56180_T6 (SEQ ID
NO:9). An alignment is given to the known protein (Calsequestrin,
cardiac muscle isoform precursor (SEQ ID NO:349)) at the end of the
application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between N56180_P7 (SEQ ID NO:289) and CAQ2_HUMAN
(SEQ ID NO:349):
1. An isolated chimeric polypeptide encoding for N56180_P7 (SEQ ID
NO:289), comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence MSSWLSAGSPSSLSV (SEQ ID NO:403)
corresponding to amino acids 1-15 of N56180_P7 (SEQ ID NO:289), and
a second amino acid sequence being at least 90% homologous to
VAKKLSLKMNEVDFYEPFMDEPIAIPNKPYTEEELVEFVKEHQRPTLRRLRPEEMFETW
EDDLNGIHIVAFAEKSDPDGYEFLEILKQVARDNTDNPDLSILWIDPDDFPLLVAYWEKT
FKIDLFRPQIGVVNVTDADSVWMEIPDDDDLPTAEELEDWIEDVLSGKINTEDDDEDDD
DDDNSDEEDNDDSDDDDDE corresponding to amino acids 203-399 of
CAQ2_HUMAN (SEQ ID NO:349), which also corresponds to amino acids
16-212 of N56180_P7 (SEQ ID NO:289), wherein said first and second
amino acid sequences are contiguous and in a sequential order.
2. An isolated polypeptide encoding for a head of N56180_P7 (SEQ ID
NO:289), comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MSSWLSAGSPSSLSV (SEQ ID NO:403) of N56180_P7 (SEQ
ID NO:289).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein N56180_P7 (SEQ ID NO:289) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 15, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein N56180_P7 (SEQ ID NO:289) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00049 TABLE 15 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
42 N -> No
Variant protein N56180_P7 (SEQ ID NO:289) is encoded by the
following transcript(s): N56180_T6 (SEQ ID NO:9), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript N56180_T6 (SEQ ID NO:9) is shown in bold;
this coding portion starts at position 71 and ends at position 706.
The transcript also has the following SNPs as listed in Table 16
(given according to their position on the nucleotide sequence, with
the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein N56180_P7 (SEQ ID NO:289) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00050 TABLE 16 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
194 A -> No 694 C -> T Yes 1191 C -> T Yes 1341 C -> G
Yes 1462 G -> T No 1662 A -> C No 1718 A -> Yes 1811 A
-> T Yes
Variant protein N56180_P8 (SEQ ID NO:290) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) N56180_T7 (SEQ ID
NO:10). An alignment is given to the known protein (Calsequestrin,
cardiac muscle isoform precursor (SEQ ID NO:349)) at the end of the
application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between N56180_P8 (SEQ ID NO:290) and CAQ2_HUMAN
(SEQ ID NO:349):
1. An isolated chimeric polypeptide encoding for N56180_P8 (SEQ ID
NO:290), comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence MCRGYSTLLNPVS (SEQ ID NO:404)
corresponding to amino acids 1-13 of N56180_P8 (SEQ ID NO:290), and
a second amino acid sequence being at least 90% homologous to
DGYEFLEILKQVARDNTDNPDLSILWIDPDDFPLLVAYWEKTFKIDLFRPQIGVVNVTD
ADSVWMEIPDDDDLPTAEELEDWIEDVLSGKINTEDDDEDDDDDDNSDEEDNDDSDD DDDE
corresponding to amino acids 280-399 of CAQ2_HUMAN (SEQ ID NO:349),
which also corresponds to amino acids 14-133 of N56180_P8 (SEQ ID
NO:290), wherein said first and second amino acid sequences are
contiguous and in a sequential order.
2. An isolated polypeptide encoding for a head of N56180_P8 (SEQ ID
NO:290), comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence MCRGYSTLLNPVS (SEQ ID NO:404) of N56180_P8 (SEQ ID
NO:290).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein N56180_P8 (SEQ ID NO:290) is encoded by the
following transcript(s): N56180_T7 (SEQ ID NO:10), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript N56180_T7 (SEQ ID NO:10) is shown in bold;
this coding portion starts at position 97 and ends at position 495.
The transcript also has the following SNPs as listed in Table 17
(given according to their position on the nucleotide sequence, with
the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein N56180_P8 (SEQ ID NO:290) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00051 TABLE 17 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
483 C -> T Yes 980 C -> T Yes 1130 C -> G Yes 1251 G ->
T No 1451 A -> C No 1507 A -> Yes 1600 A -> T Yes
Variant protein N56180_P9 (SEQ ID NO:291) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) N56180_T8 (SEQ ID
NO:11). An alignment is given to the known protein (Calsequestrin,
cardiac muscle isoform precursor (SEQ ID NO:349)) at the end of the
application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between N56180_P9 (SEQ ID NO:291) and CAQ2_HUMAN
(SEQ ID NO:349):
1. An isolated chimeric polypeptide encoding for N56180_P9 (SEQ ID
NO:291), comprising a first amino acid sequence being at least 90%
homologous to
MKRTHLFIVGIYFLSSCRAEEGLNFPTYDGKDRVVSLSEKNFKQVLKKYDLLCLYYHEP
VSSDKVTQKQFQLKEIVLELVAQVLEHKAIGFVMVDAKKEAKLAKKLGFDEEGSLYIL
KGDRTIEFDGEFAADVLVEFLLDLIEDPVEIISSKLEVQAFERIEDYIKLIGFFKSEDSEYY
KAFEEAAEHFQPYIKFFATFDKGVAKKLSLKMNEVDFYEPFMDEPIAIPNKPYTEEELVE
FVKEHQR corresponding to amino acids 1-246 of CAQ2_HUMAN (SEQ ID
NO:349), which also corresponds to amino acids 1-246 of N56180_P9
(SEQ ID NO:291), and a second amino acid sequence being at least
70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide having the sequence SRNWTQ (SEQ ID NO:405)
corresponding to amino acids 247-252 of N56180_P9 (SEQ ID NO:291),
wherein said first and second amino acid sequences are contiguous
and in a sequential order.
2. An isolated polypeptide encoding for a tail of N56180_P9 (SEQ ID
NO:291), comprising a polypeptide being at least 70%, optionally at
least about 80%, preferably at least about 85%, more preferably at
least about 90% and most preferably at least about 95% homologous
to the sequence SRNWTQ (SEQ ID NO:405) in N56180_P9 (SEQ ID
NO:291).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted or localized in the sarcoplasmic reticulum's
terminal cisternae luminal spaces of cardiac and slow skeletal
muscle cells like the WT protein. The protein localization is
believed to be secreted because both signal-peptide prediction
programs predict that this protein has a signal peptide, and
neither trans-membrane region prediction program predicts that this
protein has a trans-membrane region.
Variant protein N56180_P9 (SEQ ID NO:291) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 18, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein N56180_P9 (SEQ ID NO:291) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00052 TABLE 18 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
229 N -> No 66 T -> A Yes 76 .sup. V -> M Yes
Variant protein N56180_P9 (SEQ ID NO:291) is encoded by the
following transcript(s): N56180_T8 (SEQ ID NO:11), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript N56180_T8 (SEQ ID NO:11) is shown in bold;
this coding portion starts at position 242 and ends at position
997. The transcript also has the following SNPs as listed in Table
19 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein N56180_P9 (SEQ ID NO:291) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00053 TABLE 19 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
74 T -> No 105 T -> C Yes 1153 G -> A Yes 1170 G -> A
Yes 206 G -> A Yes 221 G -> A Yes 228 A -> C Yes 437 A
-> G Yes 467 G -> A Yes 926 A -> No 1095 A -> No 1095 A
-> T No
As noted above, cluster N56180 features 22 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster N56180_node.sub.--2 (SEQ ID NO:73) according to the
present invention is supported by 36 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7) and N56180_T8 (SEQ
ID NO:11). Table 20 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00054 TABLE 20 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 1 237 N56180_T3 (SEQ ID NO: 6) 1 237 N56180_T4 (SEQ
ID NO: 7) 1 237 N56180_T8 (SEQ ID NO: 11) 1 237
Segment cluster N56180_node.sub.--20 (SEQ ID NO:74) according to
the present invention is supported by 30 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8), N56180_T6 (SEQ ID NO:9) and N56180_T8 (SEQ ID NO:11). Table
21 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00055 TABLE 21 Segment location on transcripts Segment
starting Segment Transcript name position ending position N56180_T1
(SEQ ID NO: 5) 943 1073 N56180_T3 (SEQ ID NO: 6) 989 1119 N56180_T4
(SEQ ID NO: 7) 662 792 N56180_T5 (SEQ ID NO: 8) 374 504 N56180_T6
(SEQ ID NO: 9) 116 246 N56180_T8 (SEQ ID NO: 11) 848 978
Segment cluster N56180_node.sub.--22 (SEQ ID NO:75) according to
the present invention is supported by 3 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T8 (SEQ ID NO:11).
Table 22 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00056 TABLE 22 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T8
(SEQ ID NO: 11) 979 1259
Segment cluster N56180_node.sub.--28 (SEQ ID NO:76) according to
the present invention is supported by 1 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T7 (SEQ ID NO:10).
Table 23 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00057 TABLE 23 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T7
(SEQ ID NO: 10) 1 136
Segment cluster N56180_node.sub.--34 (SEQ ID NO:77) according to
the present invention is supported by 37 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8), N56180_T6 (SEQ ID NO:9) and N56180_T7 (SEQ ID NO:10). Table
24 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00058 TABLE 24 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 1397 1644 N56180_T3 (SEQ ID NO: 6) 1443 1690
N56180_T4 (SEQ ID NO: 7) 1116 1363 N56180_T5 (SEQ ID NO: 8) 828
1075 N56180_T6 (SEQ ID NO: 9) 570 817 N56180_T7 (SEQ ID NO: 10) 359
606
Segment cluster N56180_node.sub.--36 (SEQ ID NO:78) according to
the present invention is supported by 77 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8), N56180_T6 (SEQ ID NO:9) and N56180_T7 (SEQ ID NO:10). Table
25 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00059 TABLE 25 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 1655 2778 N56180_T3 (SEQ ID NO: 6) 1701 2824
N56180_T4 (SEQ ID NO: 7) 1374 2497 N56180_T5 (SEQ ID NO: 8) 1086
2209 N56180_T6 (SEQ ID NO: 9) 828 1951 N56180_T7 (SEQ ID NO: 10)
617 1740
Segment cluster N56180_node.sub.--4 (SEQ ID NO:79) according to the
present invention is supported by 34 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8) and N56180_T8 (SEQ ID NO:11). Table 26 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00060 TABLE 26 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 295 475 N56180_T3 (SEQ ID NO: 6) 295 475 N56180_T4
(SEQ ID NO: 7) 295 475 N56180_T5 (SEQ ID NO: 8) 34 214 N56180_T8
(SEQ ID NO: 11) 295 475
Segment cluster N56180_node.sub.--6 (SEQ ID NO:80) according to the
present invention is supported by 1 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T3 (SEQ ID NO:6).
Table 27 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00061 TABLE 27 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T3
(SEQ ID NO: 6) 476 616
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster N56180_node.sub.--0 (SEQ ID NO:81) according to the
present invention is supported by 1 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T5 (SEQ ID NO:8).
Table 28 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00062 TABLE 28 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T5
(SEQ ID NO: 8) 1 33
Segment cluster N56180_node.sub.--10 (SEQ ID NO:82) according to
the present invention is supported by 24 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7) and N56180_T8 (SEQ
ID NO:11). Table 29 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00063 TABLE 29 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 561 661 N56180_T3 (SEQ ID NO: 6) 702 802 N56180_T4
(SEQ ID NO: 7) 561 661 N56180_T8 (SEQ ID NO: 11) 561 661
Segment cluster N56180_node.sub.--12 (SEQ ID NO:83) according to
the present invention is supported by 27 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6) and N56180_T8 (SEQ ID NO:11). Table 30
below describes the starting and ending position of this segment on
each transcript.
TABLE-US-00064 TABLE 30 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 662 773 N56180_T3 (SEQ ID NO: 6) 803 914 N56180_T8
(SEQ ID NO: 11) 662 773
Segment cluster N56180_node.sub.--14 (SEQ ID NO:84) according to
the present invention is supported by 26 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T5 (SEQ ID NO:8) and N56180_T8 (SEQ
ID NO:11). Table 31 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00065 TABLE 31 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 774 847 N56180_T3 (SEQ ID NO: 6) 915 988 N56180_T5
(SEQ ID NO: 8) 300 373 N56180_T8 (SEQ ID NO: 11) 774 847
Segment cluster N56180_node.sub.--16 (SEQ ID NO:85) according to
the present invention is supported by 1 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5).
Table 32 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00066 TABLE 32 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 848 942
Segment cluster N56180_node.sub.--18 (SEQ ID NO:86) according to
the present invention is supported by 1 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T6 (SEQ ID NO:9).
Table 33 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00067 TABLE 33 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T6
(SEQ ID NO: 9) 1 115
Segment cluster N56180_node.sub.--24 (SEQ ID NO:87) according to
the present invention is supported by 25 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8) and N56180_T6 (SEQ ID NO:9). Table 34 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00068 TABLE 34 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 1074 1119 N56180_T3 (SEQ ID NO: 6) 1120 1165
N56180_T4 (SEQ ID NO: 7) 793 838 N56180_T5 (SEQ ID NO: 8) 505 550
N56180_T6 (SEQ ID NO: 9) 247 292
Segment cluster N56180_node.sub.--26 (SEQ ID NO:88) according to
the present invention is supported by 28 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8) and N56180_T6 (SEQ ID NO:9). Table 35 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00069 TABLE 35 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 1120 1174 N56180_T3 (SEQ ID NO: 6) 1166 1220
N56180_T4 (SEQ ID NO: 7) 839 893 N56180_T5 (SEQ ID NO: 8) 551 605
N56180_T6 (SEQ ID NO: 9) 293 347
Segment cluster N56180_node.sub.--29 (SEQ ID NO:89) according to
the present invention is supported by 32 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8), N56180_T6 (SEQ ID NO:9) and N56180_T7 (SEQ ID NO:10). Table
36 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00070 TABLE 36 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 1175 1275 N56180_T3 (SEQ ID NO: 6) 1221 1321
N56180_T4 (SEQ ID NO: 7) 894 994 N56180_T5 (SEQ ID NO: 8) 606 706
N56180_T6 (SEQ ID NO: 9) 348 448 N56180_T7 (SEQ ID NO: 10) 137
237
Segment cluster N56180_node.sub.--3 (SEQ ID NO:90) according to the
present invention is supported by 36 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7) and N56180_T8 (SEQ
ID NO:11). Table 37 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00071 TABLE 37 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 238 294 N56180_T3 (SEQ ID NO: 6) 238 294 N56180_T4
(SEQ ID NO: 7) 238 294 N56180_T8 (SEQ ID NO: 11) 238 294
Segment cluster N56180_node.sub.--31 (SEQ ID NO:91) according to
the present invention is supported by 30 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8), N56180_T6 (SEQ ID NO:9) and N56180_T7 (SEQ ID NO:10). Table
38 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00072 TABLE 38 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 1276 1350 N56180_T3 (SEQ ID NO: 6) 1322 1396
N56180_T4 (SEQ ID NO: 7) 995 1069 N56180_T5 (SEQ ID NO: 8) 707 781
N56180_T6 (SEQ ID NO: 9) 449 523 N56180_T7 (SEQ ID NO: 10) 238
312
Segment cluster N56180_node.sub.--33 (SEQ ID NO:92) according to
the present invention is supported by 30 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8), N56180_T6 (SEQ ID NO:9) and N56180_T7 (SEQ ID NO:10). Table
39 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00073 TABLE 39 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 1351 1396 N56180_T3 (SEQ ID NO: 6) 1397 1442
N56180_T4 (SEQ ID NO: 7) 1070 1115 N56180_T5 (SEQ ID NO: 8) 782 827
N56180_T6 (SEQ ID NO: 9) 524 569 N56180_T7 (SEQ ID NO: 10) 313
358
Segment cluster N56180_node.sub.--35 (SEQ ID NO:93) according to
the present invention can be found in the following transcript(s):
N56180_T1 (SEQ ID NO:5), N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID
NO:7), N56180_T5 (SEQ ID NO:8), N56180_T6 (SEQ ID NO:9) and
N56180_T7 (SEQ ID NO:10). Table 40 below describes the starting and
ending position of this segment on each transcript.
TABLE-US-00074 TABLE 40 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 1645 1654 N56180_T3 (SEQ ID NO: 6) 1691 1700
N56180_T4 (SEQ ID NO: 7) 1364 1373 N56180_T5 (SEQ ID NO: 8) 1076
1085 N56180_T6 (SEQ ID NO: 9) 818 827 N56180_T7 (SEQ ID NO: 10) 607
616
Segment cluster N56180_node.sub.--8 (SEQ ID NO:94) according to the
present invention is supported by 25 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): N56180_T1 (SEQ ID NO:5),
N56180_T3 (SEQ ID NO:6), N56180_T4 (SEQ ID NO:7), N56180_T5 (SEQ ID
NO:8) and N56180_T8 (SEQ ID NO:11). Table 41 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00075 TABLE 41 Segment location on transcripts Segment
Segment Transcript name starting position ending position N56180_T1
(SEQ ID NO: 5) 476 560 N56180_T3 (SEQ ID NO: 6) 617 701 N56180_T4
(SEQ ID NO: 7) 476 560 N56180_T5 (SEQ ID NO: 8) 215 299 N56180_T8
(SEQ ID NO: 11) 476 560
Variant Protein Alignment to the Previously Known Protein: Sequence
name: /tmp/QH4bp76Ojk/sAp7DyaTKD:CAQ2_HUMAN (SEQ ID NO:349)
Sequence documentation: Alignment of: N56180_P2 (SEQ ID NO:285) x
CAQ2_HUMAN (SEQ ID NO:349).
TABLE-US-00076 Alignment segment 1/1: Quality: 1955.00 Escore: 0
Matching length: 203 Total length: 203 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00009## Sequence name: /tmp/VtcMdCiEuz/FlmsgLbcq4:CAQ2_HUMAN
(SEQ ID NO:349) Sequence documentation: Alignment of: N56180_P4
(SEQ ID NO:286) x CAQ2_HUMAN (SEQ ID NO:349).
TABLE-US-00077 Alignment segment 1/1: Quality: 3806.00 Escore: 0
Matching length: 399 Total length: 446 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
89.46 Total Percent Identity: 89.46 Gaps: 1
Alignment:
##STR00010## Sequence name: /tmp/lRixkfCRfD/JDL7BwYPJs:CAQ2_HUMAN
(SEQ ID NO:349) Sequence documentation: Alignment of: N56180_P5
(SEQ ID NO:287) x CAQ2_HUMAN (SEQ ID NO:349).
TABLE-US-00078 Alignment segment 1/1: Quality: 3202.00 Escore: 0
Matching length: 337 Total length: 399 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
84.46 Total Percent Identity: 84.46 Gaps: 1
Alignment:
##STR00011## Sequence name: /tmp/rs5xPc26iA/X1zfpEDF7:CAQ2_HUMAN
(SEQ ID NO:349) Sequence documentation: Alignment of: N56180_P6
(SEQ ID NO:288) x CAQ2_HUMAN (SEQ ID NO:349).
TABLE-US-00079 Alignment segment 1/1: Quality: 2955.00 Escore: 0
Matching length: 314 Total length: 385 Matching Percent Similarity:
99.04 Matching Percent 99.04 Identity: Total Percent Similarity:
80.78 Total Percent Identity: 80.78 Gaps: 1
Alignment:
##STR00012## Sequence name: /tmp/YOj6jtvAt2/UVZXGVRVOx:CAQ2_HUMAN
(SEQ ID NO:349) Sequence documentation: Alignment of: N56180_P7
(SEQ ID NO:289) x CAQ2_HUMAN (SEQ ID NO:349).
TABLE-US-00080 Alignment segment 1/1: Quality: 1959.00 Escore: 0
Matching length: 197 Total length: 197 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00013## Sequence name: /tmp/kmYMCJ1GuB/no5BPO2sjR:CAQ2_HUMAN
(SEQ ID NO:349) Sequence documentation: Alignment of: N56180_P8
(SEQ ID NO:290) x CAQ2_HUMAN (SEQ ID NO:349).
TABLE-US-00081 Alignment segment 1/1: Quality: 1187.00 Escore: 0
Matching length: 120 Total length: 120 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00014## Sequence name: /tmp/JIYFiyYEk/C42Jok7Lfq:CAQ2_HUMAN
(SEQ ID NO:349) Sequence documentation: Alignment of: N56180_P9
(SEQ ID NO:291) x CAQ2_HUMAN (SEQ ID NO:349).
TABLE-US-00082 Alignment segment 1/1: Quality: 2388.00 Escore: 0
Matching length: 246 Total length: 246 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00015##
Expression of Calsequestrin, Cardiac Muscle Isoform Transcripts
which are Detectable by Amplicon as Depicted in Sequence Name
N56180 Specifically in Heart Tissue
Expression of Calsequestrin, cardiac muscle isoform transcripts
detectable by or according to seg6 (SEQ ID NO:335), N56180
amplicon(s) and N56180 seg6F (SEQ ID NO:279) and N56180 seg6R (SEQ
ID NO:280) primers was measured by real time PCR. In parallel the
expression of four housekeeping genes--RPL19 (GenBank Accession No.
NM.sub.--000981 (SEQ ID NO:437); RPL19 amplicon (SEQ ID NO:440)),
TATA box (GenBank Accession No. NM.sub.--003194 (SEQ ID NO:441);
TATA amplicon (SEQ ID NO:444)), Ubiquitin (GenBank Accession No.
BC000449 (SEQ ID NO:445); amplicon--Ubiquitin-amplicon (SEQ ID
NO:448)) and SDHA (GenBank Accession No. NM.sub.--004168 (SEQ ID
NO:449); amplicon--SDHA-amplicon (SEQ ID NO:452)) was measured
similarly. For each RT sample, the expression of the above
amplicons was normalized to the geometric mean of the quantities of
the housekeeping genes. The normalized quantity of each RT sample
was then divided by the median of the quantities of the heart
samples (Sample Nos. 44, 45, 46, Table 1, above, "Tissue samples in
testing panel"), to obtain a value of fold up-regulation for each
sample relative to median of the heart.
FIG. 9 is a histogram showing specific expression of the
above-indicated Calsequestrin, cardiac muscle isoform transcripts
in heart tissue samples as opposed to other tissues. As is evident
from FIG. 9, the expression of Calsequestrin, cardiac muscle
isoform transcripts detectable by the above amplicon(s) in heart
tissue samples was significantly higher than in most other samples
(non-heart tissue sample Nos. 1-21, 23-26, 28, 30-43 47-74 Table 1
above, "Tissue samples in testing panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: N56180 seg6F (SEQ ID
NO:279) forward primer; and N56180 seg6R (SEQ ID NO:280) reverse
primer.
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
N56180 seg6.
TABLE-US-00083 N56180 seg6F (SEQ ID NO:279): ATATCCCAGTGGTGGTTGCATT
N56180 seg6R (SEQ ID NO:280): CCCTCCCCAGCGTTTCC N56180 seg6 (SEQ ID
NO:335): ATATCCCAGTGGTGGTTGCATTTCCAAACCCCAAGAGAGGAAGGCAAAAT
GAAGTTGCTGGAGTTGAGTGAATCTGCAGATGGAGCTGCGTGGAAACGCT GGGGAGGG
Expression of Calsequestrin, cardiac muscle isoform transcripts
detectable by or according to seg22 node(s), N56180 amplicon(s) and
N56180 seg22F (SEQ ID NO:336) and N56180 seg22R (SEQ ID NO:337)
primers was measured by real time PCR. In parallel the expression
of four housekeeping genes--RPL19 (GenBank Accession No.
NM.sub.--000981 (SEQ ID NO:437); RPL19 amplicon (SEQ ID NO:440)),
TATA box (GenBank Accession No. NM.sub.--003194 (SEQ ID NO:441);
TATA amplicon (SEQ ID NO:444)), Ubiquitin (GenBank Accession No.
BC000449 (SEQ ID NO:445); amplicon--Ubiquitin-amplicon (SEQ ID
NO:448)) and SDHA (GenBank Accession No. NM.sub.--004168 (SEQ ID
NO:449); amplicon--SDHA-amplicon (SEQ ID NO:452)), was measured
similarly. For each RT sample, the expression of the above
amplicons was normalized to the geometric mean of the quantities of
the housekeeping genes. The normalized quantity of each RT sample
was then divided by the median of the quantities of the heart
samples (Sample Nos. 44, 45, 46, Table 1, above, "Tissue samples in
testing panel"), to obtain a value of fold up-regulation for each
sample relative to median of the heart.
FIG. 10 is a histogram showing specific expression of the
above-indicated Calsequestrin, cardiac muscle isoform transcripts
in heart tissue samples as opposed to other tissues. As is evident
from FIG. 10, the expression of Calsequestrin, cardiac muscle
isoform transcripts detectable by the above amplicon(s) in heart
tissue samples was significantly higher than in most of the other
samples (non-heart tissue sample Nos. 1-21, 23-26, 28-43, 47-74
Table 1, "Tissue samples in testing panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: N56180 seg22F (SEQ ID
NO:336) forward primer; and N56180 seg22R (SEQ ID NO:337) reverse
primer.
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
N56180 seg22.
TABLE-US-00084 N56180 seg22F (SEQ ID NO:336):
TTGATACCACTTAGTGTAGCTCCAGC N56180 seg22R (SEQ ID NO:337):
TCAAGTAGTTGCTACAGACGCCA N56180 seg22 (SEQ ID NO:361):
TTGATACCACTTAGTGTAGCTCCAGCATGGATCAGCAAACTTTTTCTGT
AAAGAACAAAATGGTAAATATTTCAGGTTCTGTGGGCCAGATGGCGTCT
GTAGCAACTACTTGA
Description for Cluster T10377
Cluster T10377 features 6 transcript(s) and 18 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00085 TABLE 1 Transcripts of interest Transcript Name Seq
ID No. T10377_T0 12 T10377_T1 13 T10377_T2 14 T10377_T5 15
T10377_T6 16 T10377_T7 17
TABLE-US-00086 TABLE 2 Segments of interest Segment Name Seq ID No.
T10377_node_0 95 T10377_node_17 96 T10377_node_19 97 T10377_node_21
98 T10377_node_27 99 T10377_node_33 100 T10377_node_12 101
T10377_node_14 102 T10377_node_16 103 T10377_node_2 104
T10377_node_23 105 T10377_node_25 106 T10377_node_29 107
T10377_node_3 108 T10377_node_31 109 T10377_node_5 110
T10377_node_8 111 T10377_node_9 112
TABLE-US-00087 TABLE 3 Proteins of interest Protein Name Seq ID No.
T10377_P2 292 T10377_P5 293 T10377_P6 294 T10377_P7 295 T10377_P8
296
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster T10377. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 11 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 11, concerning the number of
heart-specific clones in libraries/sequences.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs, which was found to be 10.9. The
expression level of this gene in muscle was negligible; and fisher
exact test P-values were computed both for library and weighted
clone counts to check that the counts are statistically
significant, and were found to be 8.60 E-15.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the expression level of this gene in
muscle was negligible, which clearly supports specific expression
in heart tissue.
As noted above, cluster T10377 features 6 transcript(s), which were
listed in Table 1 above. A description of each variant protein
according to the present invention is now provided.
Variant protein T10377_P2 (SEQ ID NO:292) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) T10377_T1 (SEQ ID
NO:13) and T10377_T2 (SEQ ID NO:14). One or more alignments to one
or more previously published protein sequences are given at the end
of the application. A brief description of the relationship of the
variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between T10377_P2 (SEQ ID NO:292) and Q96NF5 (SEQ
ID NO:362):
1. An isolated chimeric polypeptide encoding for T10377_P2 (SEQ ID
NO:292), comprising a first amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence MEISLVKCSE (SEQ ID NO:406)
corresponding to amino acids 1-10 of T10377_P2 (SEQ ID NO:292),
second amino acid sequence being at least 90% homologous to
ANVCRLRLTVPPESPVPEQCEKKIERKEQLLDLSNGEPTRKLPQGVVYGVVR
RSDQNQQKEMVVYGWSTSQLKEEMNYIKDVRATLEKVRKRMYGDYDEMR
QKIRQLTQELSVSHAQQEYLENHIQTQSSALDRFNAMNSALASDSIGLQKTL
VDVTLENSNIKDQIRNLQQTYEASMDKLREKQRQLEVAQVENQLLKMKVES
SQEANAEVMREMTKKLYSQYEEKLQEEQRKHSAEKEALLEETNSFLK corresponding to
amino acids 26-276 of Q96NF5 (SEQ ID NO:362), which also
corresponds to amino acids 11-261 of T10377_P2 (SEQ ID NO:292),
followed by A, and a third amino acid sequence being at least 90%
homologous to IEEANKKMQAAEISLEEKDQRIGELDRLIERMEKERHQLQLQLLEHETEMSG
ELTDSDKERYQQLEEASASLRERIRHLDDMVHCQQKKVKQMVEEIESLKKK
LQQKQLLILQLLEKISFLEGENNELQSRLDYLTETQAKTEVETREIGVGCDLL
PSQTGRTREIVMPSRNYTPYTRVLELTMKKTLT corresponding to amino acids
278-466 of Q96NF5 (SEQ ID NO:362), which also corresponds to amino
acids 263-451 of T10377_P2 (SEQ ID NO:292), wherein said first,
second, A, and third amino acid sequences are contiguous and in a
sequential order. 2. An isolated polypeptide encoding for a head of
T10377_P2 (SEQ ID NO:292), comprising a polypeptide being at least
70%, optionally at least about 80%, preferably at least about 85%,
more preferably at least about 90% and most preferably at least
about 95% homologous to the sequence MEISLVKCSE (SEQ ID NO:406) of
T10377_P2 (SEQ ID NO:292).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein T10377_P2 (SEQ ID NO:292) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 5, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein T10377_P2 (SEQ ID NO:292) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00088 TABLE 5 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
262 A -> V No 30 C -> S No 323 R -> G No 36 R -> K No
439 T -> No
Variant protein T10377_P2 (SEQ ID NO:292) is encoded by the
following transcript(s): T10377_T1 (SEQ ID NO:13) and T10377_T2
(SEQ ID NO:14), for which the sequence(s) is/are given at the end
of the application.
The coding portion of transcript T10377_T1 (SEQ ID NO:13) is shown
in bold; this coding portion starts at position 166 and ends at
position 1518. The transcript also has the following SNPs as listed
in Table 6 (given according to their position on the nucleotide
sequence, with the alternative nucleic acid listed; the last column
indicates whether the SNP is known or not; the presence of known
SNPs in variant protein T10377_P2 (SEQ ID NO:292) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00089 TABLE 6 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
152 A -> T Yes 253 T -> A No 272 G -> A No 624 A -> G
Yes 786 G -> A No 950 C -> T No 1077 A -> G No 1132 A
-> G No 1482 A -> No
The coding portion of transcript T10377_T2 (SEQ ID NO:14) is shown
in bold; this coding portion starts at position 270 and ends at
position 1622. The transcript also has the following SNPs as listed
in Table 7 (given according to their position on the nucleotide
sequence, with the alternative nucleic acid listed; the last column
indicates whether the SNP is known or not; the presence of known
SNPs in variant protein T10377_P2 (SEQ ID NO:292) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00090 TABLE 7 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
13 G -> T Yes 26 G -> A Yes 890 G -> A No 1054 C -> T
No 1181 A -> G No 1236 A -> G No 1586 A -> No 88 C -> T
Yes 115 G -> A Yes 126 A -> G Yes 212 A -> G No 256 A
-> T Yes 357 T -> A No 376 G -> A No 728 A -> G Yes
Variant protein T10377_P5 (SEQ ID NO:293) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) T10377_T5 (SEQ ID
NO:15).
One or more alignments to one or more previously published protein
sequences are given at the end of the application. A brief
description of the relationship of the variant protein according to
the present invention to each such aligned protein is as follows:
Comparison report between T10377_P5 (SEQ ID NO:293) and Q96NF5 (SEQ
ID NO:362): 1. An isolated chimeric polypeptide encoding for
T10377_P5 (SEQ ID NO:293), comprising a first amino acid sequence
being at least 90% homologous to
MLRSTSTVTLLSGGAARTPGAPSRRANVCRLRLTVPPESPVPEQCEKKIERKE
QLLDLSNGEPTRKLPQGVVYGVVRRSDQNQQKEMVVYGWSTSQLKEEMN
YIKDVRATLEKVRKRMYGDYDEMRQKIRQLTQELSVSHAQQEYLENHIQTQ
SSALDRFNAMNSALASDSIGLQKTLVDVTLENSNIKDQIRNLQQTYEASMDK
LREKQRQLEVAQVENQLLKMKVESSQEANAEVMREMTKKLYSQYEEKLQE
EQRKHSAEKEALLEETNSFLK corresponding to amino acids 1-276 of Q96NF5
(SEQ ID NO:362), which also corresponds to amino acids 1-276 of
T10377_P5 (SEQ ID NO:293), followed by A, a second amino acid
sequence being at least 90% homologous to
IEEANKKMQAAEISLEEKDQRIGELDRLIERMEKERHQLQLQLLEHETEMSG
ELTDSDKERYQQLEEASASLRERIRHLDDMVHCQQKKVKQMVE corresponding to amino
acids 278-372 of Q96NF5 (SEQ ID NO:362), which also corresponds to
amino acids 278-372 of T10377_P5 (SEQ ID NO:293), and a third amino
acid sequence being at least 90% homologous to
ENNELQSRLDYLTETQAKTEVETREIGVGCDLLPSQTGRTREIVMPSRNYTPY TRVLELTMKKTLT
corresponding to amino acids 401-466 of Q96NF5 (SEQ ID NO:362),
which also corresponds to amino acids 373-438 of T10377_P5 (SEQ ID
NO:293), wherein said first, A, second, and third amino acid
sequences are contiguous and in a sequential order. 2. An isolated
chimeric polypeptide encoding for an edge portion of T10377_P5 (SEQ
ID NO:293), comprising a polypeptide having a length "n", wherein n
is at least about 10 amino acids in length, optionally at least
about 20 amino acids in length, preferably at least about 30 amino
acids in length, more preferably at least about 40 amino acids in
length and most preferably at least about 50 amino acids in length,
wherein at least two amino acids comprise EE, having a structure as
follows: a sequence starting from any of amino acid numbers 372-x
to 372; and ending at any of amino acid numbers 373+((n-2)-x), in
which x varies from 0 to n-2.
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted. The protein localization is believed to be
secreted because one of the two signal-peptide prediction programs
(HMM:Signal peptide, NN:NO) predicts that this protein has a signal
peptide.
Variant protein T10377_P5 (SEQ ID NO:293) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 8, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein T10377_P5 (SEQ ID NO:293) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00091 TABLE 8 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
25 R -> G No 277 A -> V No 338 R -> G No 426 T -> No 45
C -> S No 51 R -> K No
Variant protein T10377_P5 (SEQ ID NO:293) is encoded by the
following transcript(s): T10377_T5 (SEQ ID NO:15), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript T10377_T5 (SEQ ID NO:15) is shown in bold;
this coding portion starts at position 140 and ends at position
1453. The transcript also has the following SNPs as listed in Table
9 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein T10377_P5 (SEQ ID NO:293) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00092 TABLE 9 Nucleic acid SNPs SNP position o Alternative
Previously nucleotide sequence nucleic acid known SNP? 13 G -> T
Yes 26 G -> A Yes 969 C -> T No 1096 A -> G No 1151 A
-> G No 1417 A -> No 88 C -> T Yes 115 G -> A Yes 126 A
-> G Yes 212 A -> G No 272 T -> A No 291 G -> A No 643
A -> G Yes 805 G -> A No
Variant protein T10377_P6 (SEQ ID NO:294) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) T10377_T6 (SEQ ID
NO:16).
One or more alignments to one or more previously published protein
sequences are given at the end of the application. A brief
description of the relationship of the variant protein according to
the present invention to each such aligned protein is as
follows:
Comparison report between T10377_P6 (SEQ ID NO:294) and Q96NF5 (SEQ
ID NO:362): 1. An isolated chimeric polypeptide encoding for
T10377_P6 (SEQ ID NO:294), comprising a first amino acid sequence
being at least 90% homologous to
MLRSTSTVTLLSGGAARTPGAPSRRANVCRLRLTVPPESPVPEQCEKKIERKE
QLLDLSNGEPTRKLPQGVVYGVVRRSDQNQQKEMVVYGWSTSQLKEEMN
YIKDVRATLEKVRKRMYGDYDEMRQKIRQLTQELSVSHAQQEYLENHIQTQ
SSALDRFNAMNSALASDSIGLQKTLVDVTLENSNIKDQIRNLQQTYEASMDK
LREKQRQLEVAQVENQLLKMKVESSQEANAEVMREMTKKLYSQYEEKLQE
EQRKHSAEKEALLEETNSFLK corresponding to amino acids 1-276 of Q96NF5
(SEQ ID NO:362), which also corresponds to amino acids 1-276 of
T10377_P6 (SEQ ID NO:294), followed by A, a second amino acid
sequence being at least 90% homologous to
IEEANKKMQAAEISLEEKDQRIGELDRLIERMEKERHQLQLQLLEHETEMSG
ELTDSDKERYQQLEEASASLRERIRHLDDMVHCQQKKVKQMVEEIESLKKK
LQQKQLLILQLLEKISFLEGE corresponding to amino acids 278-401 of
Q96NF5 (SEQ ID NO:362), which also corresponds to amino acids
278-401 of T10377_P6 (SEQ ID NO:294), and a third amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence PNRQDS
(SEQ ID NO:407) corresponding to amino acids 402-407 of T10377_P6
(SEQ ID NO:294), wherein said first, A, second and third amino acid
sequences are contiguous and in a sequential order. 2. An isolated
polypeptide encoding for a tail of T10377_P6 (SEQ ID NO:294),
comprising a polypeptide being at least 70%, optionally at least
about 80%, preferably at least about 85%, more preferably at least
about 90% and most preferably at least about 95% homologous to the
sequence PNRQDS (SEQ ID NO:407) in T10377_P6 (SEQ ID NO:294).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted. The protein localization is believed to be
secreted because one of the two signal-peptide prediction programs
(HMM:Signal peptide, NN:NO) predicts that this protein has a signal
peptide.
Variant protein T10377_P6 (SEQ ID NO:294) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 10, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein T10377_P6 (SEQ ID NO:294) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00093 TABLE 10 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
25 R -> G No 277 A -> V No 338 R -> G No 45 C -> S No
51 R -> K No
Variant protein T10377_P6 (SEQ ID NO:294) is encoded by the
following transcript(s): T10377_T6 (SEQ ID NO:16), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript T10377_T6 (SEQ ID NO:16) is shown in bold;
this coding portion starts at position 140 and ends at position
1360. The transcript also has the following SNPs as listed in Table
11 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein T10377_P6 (SEQ ID NO:294) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00094 TABLE 11 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
13 G -> T Yes 26 G -> A Yes 969 C -> T No 1096 A -> G
No 1151 A -> G No 1400 A -> No 88 C -> T Yes 115 G -> A
Yes 126 A -> G Yes 212 A -> G No 272 T -> A No 291 G ->
A No 643 A -> G Yes 805 G -> A No
Variant protein T10377_P7 (SEQ ID NO:295) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) T10377_T7 (SEQ ID
NO:17).
One or more alignments to one or more previously published protein
sequences are given at the end of the application. A brief
description of the relationship of the variant protein according to
the present invention to each such aligned protein is as follows:
Comparison report between T10377_P7 (SEQ ID NO:295) and Q96NF5 (SEQ
ID NO:362): 1. An isolated chimeric polypeptide encoding for
T10377_P7 (SEQ ID NO:295), comprising a first amino acid sequence
being at least 90% homologous to
MLRSTSTVTLLSGGAARTPGAPSRRANVCRLRLTVPPESPVPEQCEKKIERKE
QLLDLSNGEPTRKLPQGVVYGVVRRSDQNQQKEMVVYGWSTSQLKEEMN
YIKDVRATLEKVRKRMYGDYDEMRQKIRQLTQELSVSHAQQEYLENHIQTQ
SSALDRFNAMNSALASDSIGLQKTLVDVTLENSNIKDQIRNLQQTYEASMDK
LREKQRQLEVAQVENQLLKMKVESSQEANAEVMREMTKKLYSQYEEKLQE
EQRKHSAEKEALLEETNSFLK corresponding to amino acids 1-276 of Q96NF5
(SEQ ID NO:362), which also corresponds to amino acids 1-276 of
T10377_P7 (SEQ ID NO:295), followed by A, a second amino acid
sequence being at least 90% homologous to
IEEANKKMQAAEISLEEKDQRIGELDRLIERMEKERHQLQLQLLEHETEMSG
ELTDSDKERYQQLEEASASLRERIRHLDDMVHCQQKKVKQMVEEI corresponding to
amino acids 278-374 of Q96NF5 (SEQ ID NO:362), which also
corresponds to amino acids 278-374 of T10377_P7 (SEQ ID NO:295),
and a third amino acid sequence being at least 70%, optionally at
least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide having
the sequence MSHELFSRFSLRLFGR (SEQ ID NO:408) corresponding to
amino acids 375-390 of T10377_P7 (SEQ ID NO:295), wherein said
first, A, second and third amino acid sequences are contiguous and
in a sequential order. 2. An isolated polypeptide encoding for a
tail of T10377_P7 (SEQ ID NO:295), comprising a polypeptide being
at least 70%, optionally at least about 80%, preferably at least
about 85%, more preferably at least about 90% and most preferably
at least about 95% homologous to the sequence MSHELFSRFSLRLFGR (SEQ
ID NO:408) in T10377_P7 (SEQ ID NO:295).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted. The protein localization is believed to be
secreted because one of the two signal-peptide prediction programs
(HMM:Signal peptide, NN:NO) predicts that this protein has a signal
peptide.
Variant protein T10377_P7 (SEQ ID NO:295) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 12, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein T10377_P7 (SEQ ID NO:295) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00095 TABLE 12 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
25 R -> G No 277 A -> V No 338 R -> G No 45 C -> S No
51 R -> K No
Variant protein T10377_P7 (SEQ ID NO:295) is encoded by the
following transcript(s): T10377_T7 (SEQ ID NO:17), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript T10377_T7 (SEQ ID NO:17) is shown in bold;
this coding portion starts at position 140 and ends at position
1309. The transcript also has the following SNPs as listed in Table
13 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein T10377_P7 (SEQ ID NO:295) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00096 TABLE 13 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
13 G -> T Yes 26 G -> A Yes 969 C -> T No 1096 A -> G
No 1151 A -> G No 88 C -> T Yes 115 G -> A Yes 126 A ->
G Yes 212 A -> G No 272 T -> A No 291 G -> A No 643 A
-> G Yes 805 G -> A No
Protein T10377_P8 (SEQ ID NO:296) has an amino acid sequence as
given at the end of the application; it is encoded by transcript(s)
T10377_T0 (SEQ ID NO:12). One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between T10377_P8 (SEQ ID NO:296) and Q96NF5 (SEQ
ID NO:362):
An isolated chimeric polypeptide encoding for T10377_P8 (SEQ ID
NO:296), comprising a first amino acid sequence being at least 90%
homologous to
MEISLVKCSEANVCRLRLTVPPESPVPEQCEKKIERKEQLLDLSNGEPTRKLPQGVVYG
VVRRSDQNQQKEMVVYGWSTSQLKEEMNYIKDVRATLEKVRKRMYGDYDEMRQKIR
QLTQELSVSHAQQEYLENHIQTQSSALDRFNAMNSALASDSIGLQKTLVDVTLENSNIK
DQIRNLQQTYEASMDKLREKQRQLEVAQVENQLLKMKVESSQEANAEVMREMTKKL
YSQYEEKLQEEQRKHSAEKEALLEETNSFLK corresponding to amino acids 1-261
of Q96NF5 (SEQ ID NO:362), which also corresponds to amino acids
1-261 of T10377_P8 (SEQ ID NO:296), a second amino acid sequence
comprising A, and a third amino acid sequence being at least 90%
homologous to
IEEANKKMQAAEISLEEKDQRIGELDRLIERMEKERHQLQLQLLEHETEMSGELTDSDK
ERYQQLEEASASLRERIRHLDDMVHCQQKKVKQMVEEIESLKKKLQQKQLLILQLLEKI
SFLEGENNELQSRLDYLTETQAKTEVETREIGVGCDLLPSQTGRTREIVMPSRNYTPYTR
VLELTMKKTLT corresponding to amino acids 263-451 of Q96NF5 (SEQ ID
NO:362), which also corresponds to amino acids 263-451 of T10377_P8
(SEQ ID NO:296), wherein said first, second and third amino acid
sequences are contiguous and in a sequential order.
The location of the protein was determined according to results
from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
protein is believed to be located as follows with regard to the
cell: secreted. The protein localization is believed to be secreted
because one of the two signal-peptide prediction programs
(HMM:Signal peptide, NN:NO) predicts that this protein has a signal
peptide.
Protein T10377_P8 (SEQ ID NO:296) also has the following non-silent
SNPs (Single Nucleotide Polymorphisms) as listed in Table 14,
(given according to their position(s) on the amino acid sequence,
with the alternative amino acid(s) listed; the last column
indicates whether the SNP is known or not; the presence of known
SNPs in protein T10377_P8 (SEQ ID NO:296) sequence provides support
for the deduced sequence of this protein according to the present
invention).
TABLE-US-00097 TABLE 14 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
25 R -> G No 277 V -> A No 338 R -> G No 45 C -> S No
454 T -> No 51 R -> K No
Protein T10377_P8 (SEQ ID NO:296) is encoded by the following
transcript(s): T10377_T0 (SEQ ID NO:12), for which the sequence(s)
is/are given at the end of the application. The coding portion of
transcript T10377.sub.13 T0 (SEQ ID NO:12) is shown in bold; this
coding portion starts at position 140 and ends at position 1537.
The transcript also has the following SNPs as listed in Table 15
(given according to their position on the nucleotide sequence, with
the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
protein T10377_P8 (SEQ ID NO:296) sequence provides support for the
deduced sequence of this protein according to the present
invention).
TABLE-US-00098 TABLE 15 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
13 G -> T Yes 26 G -> A Yes 969 C -> T No 1096 A -> G
No 1151 A -> G No 1501 A -> No 88 C -> T Yes 115 G -> A
Yes 126 A -> G Yes 212 A -> G No 272 T -> A No 291 G ->
A No 643 A -> G Yes 805 G -> A No
As noted above, cluster T10377 features 18 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster T10377_node.sub.--0 (SEQ ID NO:95) according to the
present invention is supported by 25 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ ID NO:15), T10377_T6 (SEQ
ID NO:16) and T10377_T7 (SEQ ID NO:17). Table 16 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00099 TABLE 16 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 1 214 T10377_T2 (SEQ ID NO: 14) 1 214 T10377_T5
(SEQ ID NO: 15) 1 214 T10377_T6 (SEQ ID NO: 16) 1 214 T10377_T7
(SEQ ID NO: 17) 1 214
Segment cluster T10377_node.sub.--17 (SEQ ID NO:96) according to
the present invention is supported by 36 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 17 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00100 TABLE 17 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 685 817 T10377_T1 (SEQ ID NO: 13) 666 798 T10377_T2
(SEQ ID NO: 14) 770 902 T10377_T5 (SEQ ID NO: 15) 685 817 T10377_T6
(SEQ ID NO: 16) 685 817 T10377_T7 (SEQ ID NO: 17) 685 817
Segment cluster T10377_node.sub.--19 (SEQ ID NO:97) according to
the present invention is supported by 38 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 18 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00101 TABLE 18 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 818 943 T10377_T1 (SEQ ID NO: 13) 799 924 T10377_T2
(SEQ ID NO: 14) 903 1028 T10377_T5 (SEQ ID NO: 15) 818 943
T10377_T6 (SEQ ID NO: 16) 818 943 T10377_T7 (SEQ ID NO: 17) 818
943
Segment cluster T10377_node.sub.--21 (SEQ ID NO:98) according to
the present invention is supported by 42 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 19 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00102 TABLE 19 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 944 1072 T10377_T1 (SEQ ID NO: 13) 925 1053
T10377_T2 (SEQ ID NO: 14) 1029 1157 T10377_T5 (SEQ ID NO: 15) 944
1072 T10377_T6 (SEQ ID NO: 16) 944 1072 T10377_T7 (SEQ ID NO: 17)
944 1072
Segment cluster T10377_node.sub.--27 (SEQ ID NO:99) according to
the present invention is supported by 1 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T7 (SEQ ID NO:17).
Table 20 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00103 TABLE 20 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T7
(SEQ ID NO: 17) 1259 1418
Segment cluster T10377_node.sub.--33 (SEQ ID NO:100) according to
the present invention is supported by 103 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15) and T10377_T6 (SEQ ID NO:16). Table 21 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00104 TABLE 21 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 1444 2412 T10377_T1 (SEQ ID NO: 13) 1425 2393
T10377_T2 (SEQ ID NO: 14) 1529 2497 T10377_T5 (SEQ ID NO: 15) 1360
2328 T10377_T6 (SEQ ID NO: 16) 1343 2311
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster T10377_node.sub.--12 (SEQ ID NO:101) according to
the present invention is supported by 35 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 22 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00105 TABLE 22 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 458 550 T10377_T1 (SEQ ID NO: 13) 439 531 T10377_T2
(SEQ ID NO: 14) 543 635 T10377_T5 (SEQ ID NO: 15) 458 550 T10377_T6
(SEQ ID NO: 16) 458 550 T10377_T7 (SEQ ID NO: 17) 458 550
Segment cluster T10377_node.sub.--14 (SEQ ID NO:102) according to
the present invention is supported by 28 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 23 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00106 TABLE 23 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 551 664 T10377_T1 (SEQ ID NO: 13) 532 645 T10377_T2
(SEQ ID NO: 14) 636 749 T10377_T5 (SEQ ID NO: 15) 551 664 T10377_T6
(SEQ ID NO: 16) 551 664 T10377_T7 (SEQ ID NO: 17) 551 664
Segment cluster T10377_node.sub.--16 (SEQ ID NO:103) according to
the present invention can be found in the following transcript(s):
T10377_T0 (SEQ ID NO:12), T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ
ID NO:14), T10377_T5 (SEQ ID NO:15), T10377_T6 (SEQ ID NO:16) and
T10377_T7 (SEQ ID NO:17). Table 24 below describes the starting and
ending position of this segment on each transcript.
TABLE-US-00107 TABLE 24 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 665 684 T10377_T1 (SEQ ID NO: 13) 646 665 T10377_T2
(SEQ ID NO: 14) 750 769 T10377_T5 (SEQ ID NO: 15) 665 684 T10377_T6
(SEQ ID NO: 16) 665 684 T10377_T7 (SEQ ID NO: 17) 665 684
Segment cluster T10377_node.sub.--2 (SEQ ID NO:104) according to
the present invention is supported by 3 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T1 (SEQ ID NO:13).
Table 25 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00108 TABLE 25 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T1
(SEQ ID NO: 13) 1 110
Segment cluster T10377_node.sub.--23 (SEQ ID NO:105) according to
the present invention is supported by 44 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 26 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00109 TABLE 26 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 1073 1152 T10377_T1 (SEQ ID NO: 13) 1054 1133
T10377_T2 (SEQ ID NO: 14) 1158 1237 T10377_T5 (SEQ ID NO: 15) 1073
1152 T10377_T6 (SEQ ID NO: 16) 1073 1152 T10377_T7 (SEQ ID NO: 17)
1073 1152
Segment cluster T10377_node.sub.--25 (SEQ ID NO:106) according to
the present invention is supported by 50 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 27 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00110 TABLE 27 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 1153 1258 T10377_T1 (SEQ ID NO: 13) 1134 1239
T10377_T2 (SEQ ID NO: 14) 1238 1343 T10377_T5 (SEQ ID NO: 15) 1153
1258 T10377_T6 (SEQ ID NO: 16) 1153 1258 T10377_T7 (SEQ ID NO: 17)
1153 1258
Segment cluster T10377_node.sub.--29 (SEQ ID NO:107) according to
the present invention is supported by 50 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14) and T10377_T6
(SEQ ID NO:16). Table 28 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00111 TABLE 28 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 1259 1342 T10377_T1 (SEQ ID NO: 13) 1240 1323
T10377_T2 (SEQ ID NO: 14) 1344 1427 T10377_T6 (SEQ ID NO: 16) 1259
1342
Segment cluster T10377_node.sub.--3 (SEQ ID NO:108) according to
the present invention is supported by 4 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T1 (SEQ ID NO:13)
and T10377_T2 (SEQ ID NO:14). Table 29 below describes the starting
and ending position of this segment on each transcript.
TABLE-US-00112 TABLE 29 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T1
(SEQ ID NO: 13) 111 195 T10377_T2 (SEQ ID NO: 14) 215 299
Segment cluster T10377_node.sub.--31 (SEQ ID NO:109) according to
the present invention is supported by 52 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14) and T10377_T5
(SEQ ID NO:15). Table 30 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00113 TABLE 30 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 1343 1443 T10377_T1 (SEQ ID NO: 13) 1324 1424
T10377_T2 (SEQ ID NO: 14) 1428 1528 T10377_T5 (SEQ ID NO: 15) 1259
1359
Segment cluster T10377_node.sub.--5 (SEQ ID NO:110) according to
the present invention is supported by 30 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 31 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00114 TABLE 31 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 215 301 T10377_T1 (SEQ ID NO: 13) 196 282 T10377_T2
(SEQ ID NO: 14) 300 386 T10377_T5 (SEQ ID NO: 15) 215 301 T10377_T6
(SEQ ID NO: 16) 215 301 T10377_T7 (SEQ ID NO: 17) 215 301
Segment cluster T10377_node.sub.--8 (SEQ ID NO:111) according to
the present invention is supported by 35 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 32 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00115 TABLE 32 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 302 407 T10377_T1 (SEQ ID NO: 13) 283 388 T10377_T2
(SEQ ID NO: 14) 387 492 T10377_T5 (SEQ ID NO: 15) 302 407 T10377_T6
(SEQ ID NO: 16) 302 407 T10377_T7 (SEQ ID NO: 17) 302 407
Segment cluster T10377_node.sub.--9 (SEQ ID NO:112) according to
the present invention is supported by 35 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): T10377_T0 (SEQ ID NO:12),
T10377_T1 (SEQ ID NO:13), T10377_T2 (SEQ ID NO:14), T10377_T5 (SEQ
ID NO:15), T10377_T6 (SEQ ID NO:16) and T10377_T7 (SEQ ID NO:17).
Table 33 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00116 TABLE 33 Segment location on transcripts Segment
Segment Transcript name starting position ending position T10377_T0
(SEQ ID NO: 12) 408 457 T10377_T1 (SEQ ID NO: 13) 389 438 T10377_T2
(SEQ ID NO: 14) 493 542 T10377_T5 (SEQ ID NO: 15) 408 457 T10377_T6
(SEQ ID NO: 16) 408 457 T10377_T7 (SEQ ID NO: 17) 408 457
Alignment of: T10377_P2 (SEQ ID NO:292) .times.Q96NF5 (SEQ ID
NO:362)
TABLE-US-00117 Alignment segment 1/1: Quality: 4288.00 Escore: 0
Matching length: 441 Total length: 441 Matching Percent Similarity:
99.77 Matching Percent 99.77 Identity: Total Percent Similarity:
99.77 Total Percent Identity: 99.77 Gaps: 0
Alignment:
##STR00016## Alignment of: T10377_P5 (SEQ ID NO:293) .times.Q96NF 5
(SEQ ID NO:362)
TABLE-US-00118 Alignment segment 1/1: Quality: 4159.00 Escore: 0
Matching length: 438 Total length: 466 Matching Percent Similarity:
99.77 Matching Percent 99.77 Identity: Total Percent Similarity:
93.78 Total Percent Identity: 93.78 Gaps: 1
Alignment:
##STR00017## Alignment of: T10377_P6 (SEQ ID NO:294) .times.Q96NF5
(SEQ ID NO:362)
TABLE-US-00119 Alignment segment 1/1: Quality: 3896.00 Escore: 0
Matching length: 403 Total length: 403 Matching Percent Similarity:
99.50 Matching Percent 99.50 Identity: Total Percent Similarity:
99.50 Total Percent Identity: 99.50 Gaps: 0
Alignment:
##STR00018## Alignment of: T10377_P7 (SEQ ID NO:295) .times.Q96NF5
(SEQ ID NO:362)
TABLE-US-00120 Alignment segment 1/1: Quality: 3642.00 Escore: 0
Matching length: 376 Total length: 376 Matching Percent Similarity:
99.47 Matching Percent 99.47 Identity: Total Percent Similarity:
99.47 Total Percent Identity: 99.47 Gaps: 0
Alignment:
##STR00019## Alignment of: T10377_P8 (SEQ ID NO:296) .times.Q96NF5
(SEQ ID NO:362)
TABLE-US-00121 Alignment segment 1/1: Quality: 4519.00 Escore: 0
Matching length: 465 Total length: 466 Matching Percent Similarity:
99 Matching Percent 99 Identity: Total Percent Similarity: 99 Total
Percent Identity: 99 Gaps: 0
Alignment:
##STR00020## Expression of Q96NF5 Transcripts which are Detectable
by amplicon as Depicted in Sequence Name T10377 Specifically in
Heart Tissue.
Expression of Q96NF5 transcripts detectable by or according to
junc25-31 node(s), T10377 amplicon(s) and T10377 junc25-31F (SEQ ID
NO:363) and T10377 junc25-31R (SEQ ID NO:364) primers was measured
by real time PCR. In parallel the expression of four housekeeping
genes--RPL19 (GenBank Accession No. NM.sub.--000981 (SEQ ID
NO:437); RPL19 amplicon (SEQ ID NO:440)), TATA box (GenBank
Accession No. NM.sub.--003194 (SEQ ID NO:441); TATA amplicon (SEQ
ID NO:444)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID
NO:445); amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA
(GenBank Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)), was measured similarly.
For each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the median of the quantities of the heart samples
(Sample Nos. 44, 45, 46, Table 1, above "Tissue samples in testing
panel"), to obtain a value of fold up-regulation for each sample
relative to median of the heart.
FIG. 12 is a histogram showing specific expression of the
above-indicated Q96NF5 transcripts in heart tissue samples as
opposed to other tissues.
As is evident from FIG. 12, the expression of Q96NF5 transcripts
detectable by the above amplicon(s) in heart tissue samples was
significantly higher than in most other samples (non-heart tissue
sample Nos. 1-26, 28-43 47-74 Table 1, above "Tissue samples in
testing panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: T10377 junc25-31F (SEQ ID
NO:363) forward primer; and T10377 junc25-31R (SEQ ID NO:364)
reverse primer.
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
T10377 junc25-31 (SEQ ID NO:365).
TABLE-US-00122 T10377junc25-31F (SEQ ID NO:363):
AGCAGATGGTCGAGGAGAATAATG T10377junc25-31R (SEQ ID NO:364):
ATCTCTCTGGTTTCCACTTCGG T10377junc25-31 (SEQ ID NO:365):
AGCAGATGGTCGAGGAGAATAATGAACTACAAAGCAGGTTGGACTATTT
AACAGAAACCCAGGCCAAGACCGAAGTGGAAACCAGAGAGAT
Expression of Q96NF5 transcripts detectable by or according to
junc29-33 node(s), T10377 amplicon(s) and T10377 junc29-33F (SEQ ID
NO:366) and T10377 junc29-33R (SEQ ID NO:367) primers was measured
by real time PCR. In parallel the expression of four housekeeping
genes--RPL19 (GenBank Accession No. NM.sub.--000981 (SEQ ID
NO:437); RPL19 amplicon (SEQ ID NO:440)), TATA box (GenBank
Accession No. NM.sub.--003194 (SEQ ID NO:441); TATA amplicon (SEQ
ID NO:444)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID
NO:445); amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA
(GenBank Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)), was measured similarly.
For each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the median of the quantities of the heart samples
(Sample Nos. 44, 45, 46, Table 1, above "Tissue samples in testing
panel"), to obtain a value of fold up-regulation for each sample
relative to median of the heart.
FIG. 13 is a histogram showing specific expression of the
above-indicated Q96NF5 transcripts in heart tissue samples as
opposed to other tissues.
As is evident from FIG. 13, the expression of Q96NF5 transcripts
detectable by the above amplicon(s) in heart tissue samples was
significantly higher than in most other samples (non-heart tissue
sample Nos. 1-26, 28-43, 47-74 Table 1 above "Tissue samples in
testing panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: T10377 junc29-33F (SEQ ID
NO:366) forward primer; and T10377 junc29-33R (SEQ ID NO:367)
reverse primer.
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
T10377 junc29-33 (SEQ ID NO:368).
TABLE-US-00123 T10377 junc29-33F (SEQ ID NO:366):
CTTTCTTAGAAGGAGAGCCAAACAG T10377 junc29-33R (SEQ ID NO:367):
CCTAAGTCAGAGTTTTCTTCATGGTTAAC T10377 junc29-33 (SEQ ID NO:368):
CTTTCTTAGAAGGAGAGCCAAACAGGCAGGACTCGTGAAATTGTGATGCC
TTCTAGGAACTACACCCCATACACAAGAGTCCTGGAGTTAACCATGAAG
AAAACTCTGACTTAGG
Expression of Q96NF5 transcripts detectable by or according to
seg2-3 node(s), T10377 amplicon(s) and T10377 seg2-3F (SEQ ID
NO:369) and T10377 seg2-3R (SEQ ID NO:370) primers was measured by
real time PCR. In parallel the expression of four housekeeping
genes--RPL19 (GenBank Accession No. NM.sub.--000981 (SEQ ID
NO:437); RPL19 amplicon (SEQ ID NO:440)), TATA box (GenBank
Accession No. NM.sub.--003194 (SEQ ID NO:441); TATA amplicon (SEQ
ID NO:444)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID
NO:445); amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA
(GenBank Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)), was measured similarly.
For each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the median of the quantities of the heart samples
(Sample Nos. 44, 45, 46, Table 1, above "Tissue samples in testing
panel"), to obtain a value of fold up-regulation for each sample
relative to median of the heart.
FIG. 14 is a histogram showing specific expression of the
above-indicated Q96NF5 transcripts in heart tissue samples as
opposed to other tissues.
As is evident from FIG. 14, the expression of Q96NF5 transcripts
detectable by the above amplicon(s) in heart tissue samples was
significantly higher than in the skeletal muscle (non-heart tissue
sample Nos. 1-9,13-26, 28-43, 47-74 Table 1, "Tissue samples in
testing samples").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: T10377 seg2-3F (SEQ ID
NO:369) forward primer; and T10377 seg2-3R (SEQ ID NO:370) reverse
primer.
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
T10377 seg2-3 (SEQ ID NO:371).
TABLE-US-00124 T10377 seg2-3F (SEQ ID NO:369):
CTTCGCATTGTGCATAACACAA T10377 seg2-3R (SEQ ID NO:370):
GAAACTCGGATACACAATCTCCAGA T10377 seg2-3 (SEQ ID NO:371):
CTTCGCATTGTGCATAACACAAGCCCTGAACCAGCTGCTTTGGGAACCCC
TGGGAATAAAGTGCCCTACCTGCCTTTCAGGCACTGCCAAGCCTGGGGCA
TCTCTGGAGATTGTGTATCCGAGTTTC
Description for Cluster Z24874
Cluster Z24874 features 2 transcript(s) and 10 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00125 TABLE 1 Transcripts of interest Transcript Name Seq
ID No. Z24874_PEA_2_T10 18 Z24874_PEA_2_T11 19
TABLE-US-00126 TABLE 2 Segments of interest Segment Name Seq ID No.
Z24874_PEA_2_node_21 113 Z24874_PEA_2_node_4 114
Z24874_PEA_2_node_0 115 Z24874_PEA_2_node_10 116
Z24874_PEA_2_node_12 117 Z24874_PEA_2_node_13 118
Z24874_PEA_2_node_14 119 Z24874_PEA_2_node_16 120
Z24874_PEA_2_node_3 121 Z24874_PEA_2_node_6 122
TABLE-US-00127 TABLE 3 Proteins of interest Protein Name Seq ID No.
Z24874_PEA_2_P5 297 Z24874_PEA_2_P6 298
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster Z24874. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 15 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 15, concerning the number of
heart-specific clones in libraries/sequences; as well as with
regard to the histogram in FIG. 16, concerning the actual
expression of oligonucleotides in various tissues, including
heart.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs, which was found to be 16.7; the ratio of
expression of the cluster in heart specific ESTs to the overall
expression of the cluster in muscle-specific ESTs which was found
to be 2.1; and fisher exact test P-values were computed both for
library and weighted clone counts to check that the counts are
statistically significant, and were found to be 3.20 E-09.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the ratio of expression of the cluster
in heart specific ESTs to the overall expression of the cluster in
muscle-specific ESTs which was found to be 2.1, which clearly
supports specific expression in heart tissue.
As noted above, cluster Z24874 features 2 transcript(s), which were
listed in Table 1 above. A description of each variant protein
according to the present invention is now provided.
Variant protein Z24874_PEA.sub.--2_P5 (SEQ ID NO:297) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18). One or more alignments to
one or more previously published protein sequences are given at the
end of the application. A brief description of the relationship of
the variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between Z24874_PEA.sub.--2_P5 (SEQ ID NO:297) and
Q9NPI5 (SEQ ID NO:372):
1. An isolated chimeric polypeptide encoding for
Z24874_PEA.sub.--2_P5 (SEQ ID NO:297), comprising a first amino
acid sequence being at least 90% homologous to
MKLIVGIGGMTNGGKTTLTNSLLRALPNCCVIHQDDFFKPQDQIAVGEDGFKQWDVLE
SLDMEAMLDTVQAWLSSPQKFARAHGVSVQPEASDTHILLLEGFLLYSYKPLVDLYSR
RYFLTVPYEECKWRRS corresponding to amino acids 1-132 of Q9NPI5 (SEQ
ID NO:372), which also corresponds to amino acids 1-132 of
Z24874_PEA.sub.--2_P5 (SEQ ID NO:297), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
LPGRHEVPRGALP (SEQ ID NO:409) corresponding to amino acids 133-145
of Z24874_PEA.sub.--2_P5 (SEQ ID NO:297), wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
Z24874_PEA.sub.--2_P5 (SEQ ID NO:297), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
LPGRHEVPRGALP (SEQ ID NO:409) in Z24874_PEA.sub.--2_P5 (SEQ ID
NO:297).
Comparison report between Z24874_PEA.sub.--2_P5 (SEQ ID NO:297) and
Q9NZK3 (SEQ ID NO:373):
1. An isolated chimeric polypeptide encoding for
Z24874_PEA.sub.--2_P5 (SEQ ID NO:297), comprising a first amino
acid sequence being at least 90% homologous to
MKLIVGIGGMTNGGKTTLTNSLLRALPNCCVIHQDDFFKPQDQIAVGEDGFKQWDVLE
SLDMEAMLDTVQAWLSSPQKFARAHGVSVQPEASDTHILLLEGFLLYSYKP corresponding
to amino acids 1-109 of Q9NZK3 (SEQ ID NO:373), which also
corresponds to amino acids 1-109 of Z24874_PEA.sub.--2_P5 (SEQ ID
NO:297), and a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence
LVDLYSRRYFLTVPYEECKWRRSLPGRHEVPRGALP corresponding to amino acids
110-145 of Z24874_PEA.sub.--2_P5 (SEQ ID NO:297), wherein said
first and second amino acid sequences are contiguous and in a
sequential order.
2. An isolated polypeptide encoding for a tail of
Z24874_PEA.sub.--2_P5 (SEQ ID NO:297), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
LVDLYSRRYFLTVPYEECKWRRSLPGRHEVPRGALP in Z24874_PEA.sub.--2_P5 (SEQ
ID NO:297).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein Z24874_PEA.sub.--2_P5 (SEQ ID NO:297) is encoded by
the following transcript(s): Z24874_PEA.sub.--2_T10 (SEQ ID NO:18),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18) is shown in bold; this coding
portion starts at position 292 and ends at position 726. The
transcript also has the following SNPs as listed in Table 4 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein Z24874_PEA.sub.--2_P5 (SEQ ID NO:297) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00128 TABLE 4 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
1 G -> C No 70 G -> A Yes 504 C -> T No 645 C -> T Yes
954 C -> T Yes
Variant protein Z24874_PEA.sub.--2_P6 (SEQ ID NO:298) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z24874_PEA.sub.--2_T11 (SEQ ID NO:19). One or more alignments to
one or more previously published protein sequences are given at the
end of the application. A brief description of the relationship of
the variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between Z24874_PEA.sub.--2_P6 (SEQ ID NO:298) and
Q9NPI5 (SEQ ID NO:372):
1. An isolated chimeric polypeptide encoding for
Z24874_PEA.sub.--2_P6 (SEQ ID NO:298), comprising a first amino
acid sequence being at least 90% homologous to
MKLIVGIGGMTNGGKTTLTNSLLRALPNCCVIHQDDFFKPQDQIAVGEDGFKQWDVLE
SLDMEAMLDTVQAWLSSPQKFARAHGVSVQPEASDTHILLLEGFLLYSY corresponding to
amino acids 1-107 of Q9NP15 (SEQ ID NO:372), which also corresponds
to amino acids 1-107 of Z24874_PEA.sub.--2_P6 (SEQ ID NO:298), and
a second amino acid sequence being at least 70%, optionally at
least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide having
the sequence NLPGRHEVPRGALP (SEQ ID NO:410) corresponding to amino
acids 108-121 of Z24874_PEA.sub.--2_P6 (SEQ ID NO:298), wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
2. An isolated polypeptide encoding for a tail of
Z24874_PEA.sub.--2_P6 (SEQ ID NO:298), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
NLPGRHEVPRGALP (SEQ ID NO:410) in Z24874_PEA.sub.--2_P6 (SEQ ID
NO:298).
Comparison report between Z24874_PEA.sub.--2_P6 (SEQ ID NO:298) and
Q9NZK3 (SEQ ID NO:373):
1. An isolated chimeric polypeptide encoding for
Z24874_PEA.sub.--2_P6 (SEQ ID NO:298), comprising a first amino
acid sequence being at least 90% homologous to
MKLIVGIGGMTNGGKTTLTNSLLRALPNCCVIHQDDFFKPQDQIAVGEDGFKQWDVLE
SLDMEAMLDTVQAWLSSPQKFARAHGVSVQPEASDTHILLLEGFLLYSY corresponding to
amino acids 1-107 of Q9NZK3 (SEQ ID NO:373), which also corresponds
to amino acids 1-107 of Z24874_PEA.sub.--2_P6 (SEQ ID NO:298), and
a second amino acid sequence being at least 70%, optionally at
least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide having
the sequence NLPGRHEVPRGALP (SEQ ID NO:410) corresponding to amino
acids 108-121 of Z24874_PEA.sub.--2_P6 (SEQ ID NO:298), wherein
said first and second amino acid sequences are contiguous and in a
sequential order.
2. An isolated polypeptide encoding for a tail of
Z24874_PEA.sub.--2_P6 (SEQ ID NO:298), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
NLPGRHEVPRGALP (SEQ ID NO:410) in Z24874_PEA.sub.--2_P6 (SEQ ID
NO:298).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein Z24874_PEA.sub.--2_P6 (SEQ ID NO:298) is encoded by
the following transcript(s): Z24874_PEA.sub.--2_T11 (SEQ ID NO:19),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
Z24874_PEA.sub.--2_T11 (SEQ ID NO:19) is shown in bold; this coding
portion starts at position 292 and ends at position 654. The
transcript also has the following SNPs as listed in Table 5 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein Z24874_PEA.sub.--2_P6 (SEQ ID NO:298) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00129 TABLE 5 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
1 G -> C No 70 G -> A Yes 504 C -> T No 882 C -> T
Yes
As noted above, cluster Z24874 features 10 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster Z24874_PEA.sub.--2_node.sub.--21 (SEQ ID NO:113)
according to the present invention is supported by 30 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18) and Z24874_PEA.sub.--2_T11
(SEQ ID NO:19). Table 6 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00130 TABLE 6 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 (SEQ 687 1027 ID NO: 18) Z24874_PEA_2_T11 (SEQ 615
955 ID NO: 19)
Segment cluster Z24874_PEA.sub.--2_node.sub.--4 (SEQ ID NO:114)
according to the present invention is supported by 19 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18) and Z24874_PEA.sub.--2_T11
(SEQ ID NO:19). Table 7 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00131 TABLE 7 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 (SEQ 138 317 ID NO: 18) Z24874_PEA_2_T11 (SEQ 138
317 ID NO: 19)
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster Z24874_PEA.sub.--2_node.sub.--0 (SEQ ID NO:115)
according to the present invention is supported by 3 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18) and Z24874_PEA.sub.--2_T11
(SEQ ID NO:19). Table 8 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00132 TABLE 8 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 1 77 (SEQ ID NO: 18) Z24874_PEA_2_T11 1 77 (SEQ ID
NO: 19)
Segment cluster Z24874_PEA.sub.--2_node.sub.--10 (SEQ ID NO:116)
according to the present invention is supported by 25 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18) and Z24874_PEA.sub.--2_T11
(SEQ ID NO:19). Table 9 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00133 TABLE 9 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 409 457 (SEQ ID NO: 18) Z24874_PEA_2_T11 409 457
(SEQ ID NO: 19)
Segment cluster Z24874_PEA.sub.--2_node.sub.--12 (SEQ ID NO:117)
according to the present invention is supported by 26 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18) and Z24874_PEA.sub.--2_T11
(SEQ ID NO:19). Table 10 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00134 TABLE 10 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 458 524 (SEQ ID NO: 18) Z24874_PEA_2_T11 458 524
(SEQ ID NO: 19)
Segment cluster Z24874_PEA.sub.--2_node.sub.--13 (SEQ ID NO:118)
according to the present invention is supported by 21 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18) and Z24874_PEA.sub.--2_T11
(SEQ ID NO:19). Table 11 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00135 TABLE 11 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 525 561 (SEQ ID NO: 18) Z24874_PEA_2_T11 525 561
(SEQ ID NO: 19)
Segment cluster Z24874_PEA.sub.--2_node.sub.--14 (SEQ ID NO:119)
according to the present invention is supported by 20 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18) and Z24874_PEA.sub.--2_T11
(SEQ ID NO:19). Table 12 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00136 TABLE 12 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 562 614 (SEQ ID NO: 18) Z24874_PEA_2_T11 562 614
(SEQ ID NO: 19)
Segment cluster Z24874_PEA.sub.--2_node.sub.--16 (SEQ ID NO:120)
according to the present invention is supported by 17 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18). Table 13 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00137 TABLE 13 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 615 686 (SEQ ID NO: 18)
Segment cluster Z24874_PEA.sub.--2_node.sub.--3 (SEQ ID NO:121)
according to the present invention is supported by 8 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
Z24874_PEA.sub.--2_T10 (SEQ ID NO:18) and Z24874_PEA.sub.--2_T11
(SEQ ID NO:19). Table 14 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00138 TABLE 14 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 78 137 (SEQ ID NO: 18) Z24874_PEA_2_T11 78 137
(SEQ ID NO: 19)
Segment cluster Z24874_PEA.sub.--2_node.sub.--6 (SEQ ID NO:122)
according to the present invention is supported by 23 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z24874_PEA.sub.--2.sub.13 T10 (SEQ ID NO:18) and
Z24874_PEA.sub.--2_T11 (SEQ ID NO:19). Table 15 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00139 TABLE 15 Segment location on transcripts Segment
Segment Transcript name starting position ending position
Z24874_PEA_2_T10 318 408 (SEQ ID NO: 18) Z24874_PEA_2_T11 318 408
(SEQ ID NO: 19)
Variant Protein Alignment to the Previously Known Protein: Sequence
name: /tmp/Ro5LG3OhE3/oQvcWauNWJ:Q9NPI5 (SEQ ID NO:372) Sequence
documentation: Alignment of: Z24874_PEA.sub.--2_P5 (SEQ ID NO:297)
.times.Q9NPI5 (SEQ ID NO:367)
TABLE-US-00140 Alignment segment 1/1: Quality: 1307.00 Escore: 0
Matching length: 132 Total length: 132 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00021## Sequence name: /tmp/Ro5LG3OhE3/oQvcWauNWJ:Q9NZK3 (SEQ
ID NO:373) Sequence documentation: Alignment of:
Z24874_PEA.sub.--2_P5 (SEQ ID NO:297) .times.Q9NZK3 (SEQ ID
NO:373)
TABLE-US-00141 Alignment segment 1/1: Quality: 1070.00 Escore: 0
Matching length: 109 Total length: 109 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00022## Sequence name: /tmp/TxcClAWX3r/LIZBcJOujT:Q9NPI5 (SEQ
ID NO:372) Sequence documentation: Alignment of:
Z24874_PEA.sub.--2_P6 (SEQ ID NO:298) .times.Q9NPI5 (SEQ ID
NO:372)
TABLE-US-00142 Alignment segment 1/1: Quality: 1048.00 Escore: 0
Matching length: 107 Total length: 107 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00023## Sequence name: /tmp/TxcClAWX3r/LIZBcJOujT:Q9NZK3 (SEQ
ID NO:373) Sequence documentation: Alignment of:
Z24874_PEA.sub.--2_P6 (SEQ ID NO:298) .times.Q9NZK3 (SEQ ID
NO:373)
TABLE-US-00143 Alignment segment 1/1: Quality: 1048.00 Escore: 0
Matching length: 107 Total length: 107 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00024##
Description for Cluster HUMCDDANF
Cluster HUMCDDANF features 2 transcript(s) and 7 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00144 TABLE 1 Transcripts of interest Transcript Name Seq
ID No. HUMCDDANF_T3 20 HUMCDDANF_T4 21
TABLE-US-00145 TABLE 2 Segments of interest Segment Name Seq ID No.
HUMCDDANF_node_0 123 HUMCDDANF_node_10 124 HUMCDDANF_node_2 125
HUMCDDANF_node_5 126 HUMCDDANF_node_8 127 HUMCDDANF_node_11 128
HUMCDDANF_node_12 129
TABLE-US-00146 TABLE 3 Proteins of interest Protein Name Seq ID No.
HUMCDDANF_P2 299 HUMCDDANF_P3 300
These sequences are variants of the known protein Atrial
natriuretic factor precursor (SEQ ID NO:350) (SwissProt accession
identifier ANF_HUMAN; known also according to the synonyms ANF;
Atrial natriuretic peptide; ANP; Prepronatriodilatin), referred to
herein as the previously known protein; it contains
Cardiodilatin-related peptide (CDP).
Protein Atrial natriuretic factor precursor (SEQ ID NO:350) is
known or believed to have the following function(s): Atrial
natriuretic factor (ANF) is a potent vasoactive substance
synthesized in mammalian atria and is thought to play a key role in
cardiovascular homeostasis; has a cGMP-stimulating activity. The
sequence for protein Atrial natriuretic factor precursor is given
at the end of the application, as "Atrial natriuretic factor
precursor amino acid sequence" (SEQ ID NO:350). Known polymorphisms
for this sequence are as shown in Table 4.
TABLE-US-00147 TABLE 4 Amino acid mutations for Known Protein SNP
position(s) on amino acid sequence Comment 32 V -> M (in
dbSNP:5063). /FTId=VAR_014579. 152-153 Missing (in isoform 2).
/FTId=VAR_000594. 65 E -> D
Protein Atrial natriuretic factor precursor (SEQ ID NO:350)
localization is believed to be Secreted.
It has been investigated for clinical/therapeutic use in humans,
for example as a target for an antibody or small molecule, and/or
as a direct therapeutic; available information related to these
investigations is as follows. Potential pharmaceutically related or
therapeutically related activity or activities of the previously
known protein are as follows: Aldosterone antagonist; Diuretic;
Electrolyte absorption agonist. A therapeutic role for a protein
represented by the cluster has been predicted. The cluster was
assigned this field because there was information in the drug
database or the public databases (e.g., described herein above)
that this protein, or part thereof, is used or can be used for a
potential therapeutic indication: Antihypertensive, diuretic;
Antiasthma; Urological; Cardiostimulant, Antianaemic,
Cardiovascular, Neuroprotective, Fertility enhancer, Male
contraceptive, Hypolipaemic/Antiatherosclerosis, Hepatoprotective
and renal failure.
The following GO Annotation(s) apply to the previously known
protein. The following annotation(s) were found: physiological
processes; blood pressure regulation, which are annotation(s)
related to Biological Process; hormone activity, which are
annotation(s) related to Molecular Function; and extracellular,
which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the
SwissProt/TremB1 Protein knowledgebase, available from <dot
expasy dot ch/sprot/>; or Locuslink, available from <dot ncbi
dot nlm dot nih dot gov/projects/LocusLink>.
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster HUMCDDANF. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 17A refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 17A, concerning the number of
heart-specific clones in libraries/sequences; as well as with
regard to the histogram in FIG. 17B, concerning the actual
expression of oligonucleotides in various tissues, including
heart.
This cluster was found to be selectively expressed in heart for the
following reasons: a comparison of the ratio of expression of the
cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs was found to be 56.3; The expression
levels of this gene in muscle was negligible; and fisher exact test
P-values were computed both for library and weighted clone counts
to check that the counts are statistically significant, and were
found to be 1.20 E-249.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the expression levels of this gene in
muscle was negligible, which clearly supports specific expression
in heart tissue.
As noted above, cluster HUMCDDANF features 2 transcript(s), which
were listed in Table 1 above. These transcript(s) encode for
protein(s) which are variant(s) of protein Atrial natriuretic
factor precursor (SEQ ID NO:350). A description of each variant
protein according to the present invention is now provided.
Variant protein HUMCDDANF_P2 (SEQ ID NO:299) according to the
present invention has an amino acid sequence as given at the end of
the application; it is encoded by transcript(s) HUMCDDANF_T3 (SEQ
ID NO:20). An alignment is given to the known protein (Atrial
natriuretic factor precursor (SEQ ID NO:350)) at the end of the
application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between HUMCDDANF_P2 (SEQ ID NO:299) and
ANF_HUMAN (SEQ ID NO:350):
1. An isolated chimeric polypeptide encoding for HUMCDDANF_P2 (SEQ
ID NO:299), comprising a first amino acid sequence being at least
90% homologous to
MPLEDEVVPPQVLSEPNEEAGAALSPLPEVPPWTGEVSPAQRDGGALGRGPWDSSDRS
ALLKSKLRALLTAPRSLRRSSCFGGRMDRIGAQSGLGCNSFRY corresponding to amino
acids 51-151 of ANF_HUMAN (SEQ ID NO:350), which also corresponds
to amino acids 1-101 of HUMCDDANF_P2 (SEQ ID NO:299).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HUMCDDANF_P2 (SEQ ID NO:299) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 7, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein HUMCDDANF_P2 (SEQ ID NO:299) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00148 TABLE 7 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
20 A -> V Yes 27 L -> F Yes 74 S -> No 76 R -> Q
Yes
Variant protein HUMCDDANF_P2 (SEQ ID NO:299) is encoded by the
following transcript(s): HUMCDDANF_T3 (SEQ ID NO:20), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript HUMCDDANF_T3 (SEQ ID NO:20) is shown in bold;
this coding portion starts at position 381 and ends at position
683. The transcript also has the following SNPs as listed in Table
8 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein HUMCDDANF_P2 (SEQ ID NO:299) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00149 TABLE 8 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
199 C -> T Yes 374 A -> G No 771 T -> C Yes 778 T -> C
Yes 809 C -> T Yes 887 C -> G No 968 A -> C Yes 439 C
-> T Yes 458 C -> T No 459 C -> T Yes 602 C -> No 607 G
-> A Yes 684 T -> C Yes (short/long variant) 711 A -> G No
757 G -> T Yes
Variant protein HUMCDDANF_P3 (SEQ ID NO:300) according to the
present invention has an amino acid sequence as given at the end of
the application; it is encoded by transcript(s) HUMCDDANF_T4 (SEQ
ID NO:21). An alignment is given to the known protein (Atrial
natriuretic factor precursor (SEQ ID NO:350)) at the end of the
application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between HUMCDDANF_P3 (SEQ ID NO:300) and
ANF_HUMAN (SEQ ID NO:350):
1. An isolated chimeric polypeptide encoding for HUMCDDANF_P3 (SEQ
ID NO:300), comprising a first amino acid sequence being at least
70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide having the sequence MSSFSTTT (SEQ ID NO:411)
corresponding to amino acids 1-8 of HUMCDDANF_P3 (SEQ ID NO:300),
and a second amino acid sequence being at least 90% homologous to
NLLDHLEEKMPLEDEVVPPQVLSEPNEEAGAALSPLPEVPPWTGEVSPAQRDGGALGR
GPWDSSDRSALLKSKLRALLTAPRSLRRSSCFGGRMDRIGAQSGLGCNSFRY corresponding
to amino acids 42-151 of ANF_HUMAN (SEQ ID NO:350), which also
corresponds to amino acids 9-118 of HUMCDDANF_P3 (SEQ ID NO:300),
wherein said first and second amino acid sequences are contiguous
and in a sequential order.
2. An isolated polypeptide encoding for a head of HUMCDDANF_P3 (SEQ
ID NO:300), comprising a polypeptide being at least 70%, optionally
at least about 80%, preferably at least about 85%, more preferably
at least about 90% and most preferably at least about 95%
homologous to the sequence MSSFSTTT (SEQ ID NO:411) of HUMCDDANF_P3
(SEQ ID NO:300)
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HUMCDDANF_P3 (SEQ ID NO:300) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 9, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein HUMCDDANF_P3 (SEQ ID NO:300) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00150 TABLE 9 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
37 A -> V Yes 44 L -> F Yes 91 S -> No 93 R -> Q
Yes
Variant protein HUMCDDANF_P3 (SEQ ID NO:300) is encoded by the
following transcript(s): HUMCDDANF_T4 (SEQ ID NO:21), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript HUMCDDANF_T4 (SEQ ID NO:21) is shown in bold;
this coding portion starts at position 104 and ends at position
457. The transcript also has the following SNPs as listed in Table
10 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein HUMCDDANF_P3 (SEQ ID NO:300) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00151 TABLE 10 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
148 A -> G No 213 C -> T Yes 552 T -> C Yes 583 C -> T
Yes 661 C -> G No 742 A -> C Yes 232 C -> T No 233 C ->
T Yes 376 C -> No 381 G -> A Yes 458 T -> C Yes
(short/long isoform) 485 A -> G No 531 G -> T Yes 545 T ->
C Yes
As noted above, cluster HUMCDDANF features 7 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster HUMCDDANF_node.sub.--0 (SEQ ID NO:123) according to
the present invention is supported by 5 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMCDDANF_T3 (SEQ ID
NO:20). Table 11 below describes the starting and ending position
of this segment on each transcript.
TABLE-US-00152 TABLE 11 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMCDDANF_T3 1 353 (SEQ ID NO: 20)
Segment cluster HUMCDDANF_node.sub.--10 (SEQ ID NO:124) according
to the present invention is supported by 49 libraries. The number
of libraries was determined as previously described. This segment
can be found in the following transcript(s): HUMCDDANF_T3 (SEQ ID
NO:20) and HUMCDDANF_T4 (SEQ ID NO:21). Table 12 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00153 TABLE 12 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMCDDANF_T3 813 940 (SEQ ID NO: 20) HUMCDDANF_T4 587 714 (SEQ ID
NO: 21)
Segment cluster HUMCDDANF_node.sub.--2 (SEQ ID NO:125) according to
the present invention is supported by 41 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMCDDANF_T4 (SEQ ID
NO:21). Table 13 below describes the starting and ending position
of this segment on each transcript.
TABLE-US-00154 TABLE 13 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMCDDANF_T4 1 127 (SEQ ID NO: 21)
Segment cluster HUMCDDANF_node.sub.--5 (SEQ ID NO:126) according to
the present invention is supported by 62 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMCDDANF_T3 (SEQ ID
NO:20) and HUMCDDANF_T4 (SEQ ID NO:21). Table 14 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00155 TABLE 14 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMCDDANF_T3 354 680 (SEQ ID NO: 20) HUMCDDANF_T4 128 454 (SEQ ID
NO: 21)
Segment cluster HUMCDDANF_node.sub.--8 (SEQ ID NO:127) according to
the present invention is supported by 56 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMCDDANF_T3 (SEQ ID
NO:20) and HUMCDDANF_T4 (SEQ ID NO:21). Table 15 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00156 TABLE 15 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMCDDANF_T3 681 812 (SEQ ID NO: 20) HUMCDDANF_T4 455 586 (SEQ ID
NO: 21)
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster HUMCDDANF_node.sub.--11 (SEQ ID NO:128) according
to the present invention can be found in the following
transcript(s): HUMCDDANF_T3 (SEQ ID NO:20) and HUMCDDANF_T4 (SEQ ID
NO:21). Table 16 below describes the starting and ending position
of this segment on each transcript.
TABLE-US-00157 TABLE 16 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMCDDANF_T3 941 951 (SEQ ID NO: 20) HUMCDDANF_T4 715 725 (SEQ ID
NO: 21)
Segment cluster HUMCDDANF_node.sub.--12 (SEQ ID NO:129) according
to the present invention is supported by 36 libraries. The number
of libraries was determined as previously described. This segment
can be found in the following transcript(s): HUMCDDANF_T3 (SEQ ID
NO:20) and HUMCDDANF_T4 (SEQ ID NO:21). Table 17 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00158 TABLE 17 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMCDDANF_T3 952 992 (SEQ IDNO: 20) HUMCDDANF_T4 726 766 (SEQ IDNO:
21)
Variant protein alignment to the previously known protein: Sequence
name: /tmp/3GyiZQyJ8L/jYng3zFfcE:ANF_HUMAN (SEQ ID NO:350) Sequence
documentation: Alignment of: HUMCDDANF_P2 (SEQ ID NO:299)
.times.ANF_HUMAN (SEQ ID NO:350)
TABLE-US-00159 Alignment segment 1/1: Quality: 988.00 Escore: 0
Matching length: 101 Total length: 101 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00025## Sequence name: /tmp/mnb7OPVCPP/oTrSwgJLyB:ANF_HUMAN
(SEQ ID NO:350) Sequence documentation: Alignment of: HUMCDDANF_P3
(SEQ ID NO:300) .times.ANF_HUMAN (SEQ ID NO:350)
TABLE-US-00160 Alignment segment 1/1: Quality: 1076.00 Escore: 0
Matching length: 110 Total length: 110 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00026##
Expression of Human Cardiodilatin-Atrial Natriuretic Factor
(CDD-ANF) HUMCDDANF Transcripts which are Detectable by Amplicon as
Depicted in Sequence Name HUHUMCDDANFjunc2-5F2R2 (SEQ ID NO:376)
Specifically in Heart Tissue
Expression of Human cardiodilatin-atrial natriuretic factor
(CDD-ANF) transcripts detectable by or according to junc2-5
node(s), HUHUMCDDANFjunc2-5F2R2 (SEQ ID NO:376) amplicon and
primers HUMCDDANFjunc2-5F2 (SEQ ID NO:374) HUMCDDANFjunc2-5R2 (SEQ
ID NO:375) was measured by real time PCR (this transcript relates
to the known or WT protein). In parallel the expression of four
housekeeping genes--RPL19 (GenBank Accession No. NM.sub.--000981
(SEQ ID NO:437); RPL19 amplicon (SEQ ID NO:440)), TATA box (GenBank
Accession No. NM.sub.--003194 (SEQ ID NO:441); TATA amplicon (SEQ
ID NO:444)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID
NO:445); amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA
(GenBank Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)) was measured similarly.
For each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the quantity of heart sample no. 45 (Table 1,
above), to obtain a value of relative expression for each sample
relative to this heart sample.
As is evident from FIG. 18, the expression of Human
cardiodilatin-atrial natriuretic factor (CDD-ANF) transcripts
detectable by the above amplicon(s) in one of the heart tissue
samples (Sample Nos. 45, Table 1, "Tissue samples in testing
panel") was significantly higher than in the other samples,
including other two heart samples. Sample 45 is from fibrotic
heart, as opposed to heart samples 44 and 46 that are from normal
hearts. (Note--the product in samples 10 and 11 was found to be a
non-specific product by inspecting the dissociation curve that was
created in the real-time PCR experiment).
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: HUMCDDANFjunc2-5F2 (SEQ ID
NO:374) forward primer; and HUMCDDANFjunc2-5R2 (SEQ ID NO:375)
reverse primer.
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
HUHUMCDDANFjunc2-5F2R2 (SEQ ID NO:376).
TABLE-US-00161 Forward primer HUMCDDANFjunc2-5F2 (SEQ ID NO:374):
CTTCTCCACCACCACCAATTTG Reverse primer HUMCDDANFjunc2-5R2 (SEQ ID
NO:375): GAGAGCAGCCCCCGCT Amplicon HUMCDDANFjunc2-5F2R2 (SEQ ID
NO:376): CTTCTCCACCACCACCAATTTGCTGGACCATTTGGAAGAAAAGATGCCTT
TAGAAGATGAGGTCGTGCCCCCACAAGTGCTCAGTGAGCCGAATGAAGAA
GCGGGGGCTGCTCTC
Description for Cluster HUMTROPIA
Cluster HUMTROPIA features 4 transcript(s) and 20 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00162 TABLE 1 Transcripts of interest Transcript Name Seq
ID No. HUMTROPIA_PEA_2_T10 22 HUMTROPIA_PEA_2_T15 23
HUMTROPIA_PEA_2_T3 24 HUMTROPIA_PEA_2_T7 25
TABLE-US-00163 TABLE 2 Segments of interest Segment Name Seq ID No.
HUMTROPIA_PEA_2_node_0 130 HUMTROPIA_PEA_2_node_10 131
HUMTROPIA_PEA_2_node_22 132 HUMTROPIA_PEA_2_node_23 133
HUMTROPIA_PEA_2_node_11 134 HUMTROPIA_PEA_2_node_14 135
HUMTROPIA_PEA_2_node_15 136 HUMTROPIA_PEA_2_node_16 137
HUMTROPIA_PEA_2_node_20 138 HUMTROPIA_PEA_2_node_21 139
HUMTROPIA_PEA_2_node_24 140 HUMTROPIA_PEA_2_node_25 141
HUMTROPIA_PEA_2_node_29 142 HUMTROPIA_PEA_2_node_30 143
HUMTROPIA_PEA_2_node_31 144 HUMTROPIA_PEA_2_node_32 145
HUMTROPIA_PEA_2_node_4 146 HUMTROPIA_PEA_2_node_5 147
HUMTROPIA_PEA_2_node_8 148 HUMTROPIA_PEA_2_node_9 149
TABLE-US-00164 TABLE 3 Proteins of interest Protein Name Seq ID No.
HUMTROPIA_PEA_2_P5 301 HUMTROPIA_PEA_2_P12 302 HUMTROPIA_PEA_2_P17
303 HUMTROPIA_PEA_2_P18 304
These sequences are variants of the known protein Troponin I,
cardiac muscle (SwissProt accession identifier TRIC_HUMAN),
referred to herein as the previously known protein and shown as SEQ
ID NO: 351.
Protein Troponin I, cardiac muscle (SEQ ID NO:351) is known or
believed to have the following function(s): Troponin I is the
inhibitory subunit of troponin, the thin filament regulatory
complex which confers calcium-sensitivity to striated muscle
actomyosin ATPase activity. Troponin I, cardiac muscle (SEQ ID
NO:351) Binds to actin and tropomyosin. Defects in Troponin I,
cardiac muscle (SEQ ID NO:351) are the cause of familial
hypertrophic cardiomyopathy type 7 (CMH7) [MIM:191044]; also known
as FHC type 7. CMH7 is an autosomal dominant disorder characterized
by increased myocardial mass with myocyte and myofibrillar
disarray. Defects in Troponin I, cardiac muscle (SEQ ID NO:351) are
the cause of familial restrictive cardiomyopathy (RCM)
[MIM:115210]. RCM is a heart muscle disorder characterized by
impaired filling of the ventricles with reduced volume in the
presence of normal or near normal wall thickness and systolic
function. The disease may be associated with systemic disease but
is most often idiopathic. The sequence for protein Troponin I,
cardiac muscle is given at the end of the application, as "Troponin
I, cardiac muscle amino acid sequence" (SEQ ID NO:351). Known
polymorphisms for this sequence are as shown in Table 4.
TABLE-US-00165 TABLE 4 Amino acid mutations for Known Protein SNP
position(s) on amino acid sequence Comment 81 P -> S (in CMH7).
/FTId=VAR_016078. 143 L -> Q (in RCM). /FTId=VAR_016079. 144 R
-> G (in CMH7). /FTId=VAR_007603. 144 R -> W (in RCM).
/FTId=VAR_016080. 170 A -> T (in RCM). /FTId=VAR_016081. 177 K
-> E (in RCM). /FTId=VAR_016082. 189 D -> H (in CMH7 and
RCM). /FTId = VAR_016083. 191 R -> H (in RCM). /FTId=VAR_016084.
195 D -> N (in CMH7). /FTId=VAR_016085. 205 K -> Q (in CMH7).
/FTId=VAR_007604.
In addition to the above known polymorphisms, the present inventors
have uncovered two new additional SNPs (shown with regard to SEQ ID
NO:352 for the resultant amino acid sequence, and SEQ ID NO:353 for
the nucleic acid sequence). This SNP is C->(missing nucleotide
"C"; will affect amino acid residues from 167 onwards). This will
create a frame shift. A new protein will be formed. However, this
SNP was located in a stretch of cytosine residues, which are known
to be prone to errors in sequencing.
The previously known protein also has the following indication(s)
and/or potential therapeutic use(s): Cancer, lung, non-small cell;
Cancer, breast; Cancer, sarcoma. It has been investigated for
clinical/therapeutic use in humans, for example as a target for an
antibody or small molecule, and/or as a direct therapeutic;
available information related to these investigations is as
follows. Potential pharmaceutically related or therapeutically
related activity or activities of the previously known protein are
as follows: Angiogenesis inhibitor; Epidermal growth factor
antagonist; Fibroblast growth factor receptor antagonist. A
therapeutic role for a protein represented by the cluster has been
predicted. The cluster was assigned this field because there was
information in the drug database or the public databases (e.g.,
described herein above) that this protein, or part thereof, is used
or can be used for a potential therapeutic indication:
Ophthalmological; Anticancer.
The following GO Annotation(s) apply to the previously known
protein. The following annotation(s) were found: control of heart,
which are annotation(s) related to Biological Process; and troponin
complex, which are annotation(s) related to Cellular Component.
The GO assignment relies on information from one or more of the
SwissProt/TremB1Protein knowledgebase, available from <dot
expasy dot ch/sprot/>; or Locuslink, available from <dot ncbi
dot nlm dot nih dot gov/projects/LocusLink/>.
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster HUMTROPIA. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 19 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 19, concerning the number of
heart-specific clones in libraries/sequences; as well as with
regard to the histogram in FIG. 20, concerning the actual
expression of oligonucleotides in various tissues, including
heart.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs, which was found to be 27.5. The
expression level of this gene in muscle was negligible; and fisher
exact test P-values were computed both for library and weighted
clone counts to check that the counts are statistically
significant, and were found to be 2.10E-88.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the expression level of this gene in
muscle was negligible which clearly supports specific expression in
heart tissue.
As noted above, cluster HUMTROPIA features 4 transcript(s), which
were listed in Table 1 above. These transcript(s) encode for
protein(s) which are variant(s) of protein Troponin I, cardiac
muscle (SEQ ID NO:351). A description of each variant protein
according to the present invention is now provided.
Variant protein HUMTROPIA_PEA.sub.--2_P5 (SEQ ID NO:301) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24). An alignment is given to
the known protein (Troponin I, cardiac muscle (SEQ ID NO:351)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between HUMTROPIA_PEA.sub.--2_P5 (SEQ ID NO:301)
and TRIC_HUMAN (SEQ ID NO:351):
1. An isolated chimeric polypeptide encoding for
HUMTROPIA_PEA.sub.--2_P5 (SEQ ID NO:301), comprising a first amino
acid sequence being at least 90% homologous to
MADGSSDAAREPRPAPAPIRRRSSNYRAYATEPHAKKKSKISASRKLQLKTLLLQIAKQ
ELEREAEERRGEKGRALSTRCQPLELAGLGFAELQDLCRQLHARVDKVDEERYDIEAK VTKNITE
corresponding to amino acids 1-124 of TRIC_HUMAN (SEQ ID NO:351),
which also corresponds to amino acids 1-124 of
HUMTROPIA_PEA.sub.--2_P5 (SEQ ID NO:301), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
VGRMGSSGTFGVG (SEQ ID NO:412) corresponding to amino acids 125-137
of HUMTROPIA_PEA.sub.--2_P5 (SEQ ID NO:301), wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
HUMTROPIA_PEA.sub.--2_P5 (SEQ ID NO:301), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VGRMGSSGTFGVG (SEQ ID NO:412) in HUMTROPIA_PEA.sub.--2_P5 (SEQ ID
NO:301).
The cellular location of the variant protein was determined
according to results from a number of different software programs
and analyses, including analyses from SignalP and other specialized
programs. The variant protein is believed to be located as follows
with regard to the cell: intracellularly. The protein localization
is believed to be intracellular because neither of the
trans-membrane region prediction programs predicted a
trans-membrane region for this protein. In addition both
signal-peptide prediction programs predict that this protein is a
non-secreted protein.
Variant protein HUMTROPIA_PEA.sub.--2_P5 (SEQ ID NO:301) is encoded
by the following transcript(s): HUMTROPIA_PEA.sub.--2_T3 (SEQ ID
NO:24), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24) is shown in bold; this
coding portion starts at position 148 and ends at position 558.
Variant protein HUMTROPIA_PEA.sub.--2_P12 (SEQ ID NO:302) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HUMTROPIA_PEA.sub.--2_T15 (SEQ ID NO:23). An alignment is given to
the known protein (Troponin I, cardiac muscle (SEQ ID NO:351)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between HUMTROPIA_PEA.sub.--2_P12 (SEQ ID NO:302)
and TRIC_HUMAN (SEQ ID NO:351):
1. An isolated chimeric polypeptide encoding for
HUMTROPIA_PEA.sub.--2_P12 (SEQ ID NO:302), comprising a first amino
acid sequence being at least 90% homologous to MADGSSDA
corresponding to amino acids 1-8 of TRIC_HUMAN (SEQ ID NO:351),
which also corresponds to amino acids 1-8 of
HUMTROPIA_PEA.sub.--2_P12 (SEQ ID NO:302), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
KKSKISASRKLQLKTLLLQIAKQELEREAEERRGEKGRALSTRCQPLELAGL
GFAELQDLCRQLHARVDKVDEERYDIEAKVTKNITEIADLTQKIFDLRGKFKRPTLRRV
RISADAMMQALLGARAKESLDLRAHLKQVKKEDTEKENREVGDWRKNIDALSGMEG RKKKFES
corresponding to amino acids 36-209 of TRIC_HUMAN (SEQ ID NO:351),
which also corresponding to amino acids 9-182 of
HUMTROPIA_PEA.sub.--2_P12 (SEQ ID NO:302), wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
2. An isolated chimeric polypeptide encoding for an edge portion of
HUMTROPIA_PEA.sub.--2_P12 (SEQ ID NO:302), comprising a polypeptide
having a length "n", wherein "n" is at least about 10 amino acids
in length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably
at least about 40 amino acids in length and most preferably at
least about 50 amino acids in length, wherein at least two amino
acids comprise AK, having a structure as follows: a sequence
starting from any of amino acid numbers 8-x to 8; and ending at any
of amino acid numbers 9+((n-2)-x), in which x varies from 0 to
n-2.
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HUMTROPIA_PEA.sub.--2_P12 (SEQ ID NO:302) is
encoded by the following transcript(s): HUMTROPIA_PEA.sub.--2_T 15
(SEQ ID NO:23), for which the sequence(s) is/are given at the end
of the application. The coding portion of transcript
HUMTROPIA_PEA.sub.--2_T115 (SEQ ID NO:23) is shown in bold; this
coding portion starts at position 148 and ends at position 693.
Variant protein HUMTROPIA_PEA.sub.--2_P17 (SEQ ID NO:303) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). An alignment is given to
the known protein (Troponin I, cardiac muscle (SEQ ID NO:351)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between HUMTROPIA_PEA.sub.--2_P17 (SEQ ID NO:303)
and TRIC_HUMAN (SEQ ID NO:351):
1. An isolated chimeric polypeptide encoding for
HUMTROPIA_PEA.sub.--2_P17 (SEQ ID NO:303), comprising a first amino
acid sequence being at least 90% homologous to
MADGSSDAAREPRPAPAPIRRRSSNYRAYATEPHAK corresponding to amino acids
1-36 of TRIC_HUMAN (SEQ ID NO:351), which also corresponds to amino
acids 1-36 of HUMTROPIA_PEA.sub.--2_P17 (SEQ ID NO:303), and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence VGRGFLGAEYRRRRDPRPWEWGEEPGLRRGRGLRGGASGAEFCRGSCSDW (SEQ ID
NO:413) corresponding to amino acids 37-86 of
HUMTROPIA_PEA.sub.--2_P17 (SEQ ID NO:303), wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
HUMTROPIA_PEA.sub.--2_P17 (SEQ ID NO:303), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VGRGFLGAEYRRRRDPRPWEWGEEPGLRRGRGLRGGASGAEFCRGSCSDW (SEQ ID NO:413)
in HUMTROPIA_PEA.sub.--2_P17 (SEQ ID NO:303).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HUMTROPIA_PEA.sub.--2_P17 (SEQ ID NO:303) is
encoded by the following transcript(s): HUMTROPIA_PEA.sub.--2_T7
(SEQ ID NO:25), for which the sequence(s) is/are given at the end
of the application. The coding portion of transcript
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25) is shown in bold; this
coding portion starts at position 148 and ends at position 405.
Variant protein HUMTROPIA_PEA.sub.--2_P18 (SEQ ID NO:304) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22). An alignment is given to
the known protein (Troponin I, cardiac muscle (SEQ ID NO:351)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between HUMTROPIA_PEA.sub.--2_P18 (SEQ ID NO:304)
and TRIC_HUMAN (SEQ ID NO:351):
1. An isolated chimeric polypeptide encoding for
HUMTROPIA_PEA.sub.--2_P18 (SEQ ID NO:304), comprising a first amino
acid sequence being at least 90% homologous to MADGSSDA
corresponding to amino acids 1-8 of TRIC_HUMAN (SEQ ID NO:351),
which also corresponds to amino acids 1-8 of
HUMTROPIA_PEA.sub.--2_P18 (SEQ ID NO:304), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence VRAAG
(SEQ ID NO:414) corresponding to amino acids 9-13 of
HUMTROPIA_PEA.sub.--2_P118 (SEQ ID NO:304), wherein said first and
second amino acid sequences are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
HUMTROPIA_PEA.sub.--2_P18 (SEQ ID NO:304), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence VRAAG (SEQ
ID NO:414) in HUMTROPIA_PEA.sub.--2_P18 (SEQ ID NO:304).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HUMTROPIA_PEA.sub.--2_P18 (SEQ ID NO:304) is
encoded by the following transcript(s): HUMTROPIA_PEA.sub.--2_T10
(SEQ ID NO:22), for which the sequence(s) is/are given at the end
of the application. The coding portion of transcript
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22) is shown in bold; this
coding portion starts at position 148 and ends at position 186.
As noted above, cluster HUMTROPIA features 20 segment(s), which
were listed in Table 2 above and for which the sequence(s) are
given at the end of the application. These segment(s) are portions
of nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--0 (SEQ ID NO:130)
according to the present invention is supported by 29 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T15
(SEQ ID NO:23), HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25), Table 7 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00166 TABLE 7 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 1 158 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 1 158
(SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 1 158 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 1 158 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--10 (SEQ ID NO:131)
according to the present invention is supported by 5 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 8 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00167 TABLE 8 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T7 256 660 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--22 (SEQ ID NO:132)
according to the present invention is supported by 8 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24). Table 9 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00168 TABLE 9 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T3 520 1053 (SEQ ID NO: 24)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--23 (SEQ ID NO:133)
according to the present invention is supported by 49 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T15
(SEQ ID NO:23), HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25), Table 10 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00169 TABLE 10 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 565 708 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 436
579 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 1054 1197 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 925 1068 (SEQ ID NO: 25)
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--11 (SEQ ID NO:134)
according to the present invention is supported by 28 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T15
(SEQ ID NO:23), HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 11 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00170 TABLE 11 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 301 342 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 172
213 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 256 297 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 661 702 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--14 (SEQ ID NO:135)
according to the present invention is supported by 37 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T15
(SEQ ID NO:23), HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 12 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00171 TABLE 12 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 343 378 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 214
249 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 298 333 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 703 738 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--15 (SEQ ID NO:136)
according to the present invention is supported by 42 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T15
(SEQ ID No:23), HUMTROPIA_PEA.sub.--2.sub.13 T3 (SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 13 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00172 TABLE 13 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 379 422 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 250
293 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 334 377 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 739 782 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--16 (SEQ ID NO:137)
according to the present invention is supported by 40 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T15
(SEQ ID NO:23), HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 14 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00173 TABLE 14 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 423 474 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 294
345 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 378 429 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 783 834 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--20 (SEQ ID NO:138)
according to the present invention is supported by 44 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T15
(SEQ ID NO:23), HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 15 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00174 TABLE 15 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 475 510 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 346
381 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 430 465 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 835 870 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--21 (SEQ ID NO:139)
according to the present invention is supported by 44 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22),
HUMTROPIA_PEA.sub.--2.sub.13 T15 (SEQ ID NO:23),
HUMTROPIA_PEA.sub.--2_T3 (SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 16 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00175 TABLE 16 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 511 564 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 382
435 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 466 519 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 871 924 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--24 (SEQ ID NO:140)
according to the present invention can be found in the following
transcript(s): HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22),
HUMTROPIA_PEA.sub.--2_T5 (SEQ ID NO:23),
HUMTROPIA_PEA.sub.--2_T10(SEQ NO:24) and HUMTROPIA_PEA.sub.--2_T7
(SEQ ID NO:25). Table 17 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00176 TABLE 17 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 709 726 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 580
597 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 1198 1215 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 1069 1086 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--25 (SEQ ID NO:141)
according to the present invention can be found in the following
transcript(s): HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22),
HUMTROPIA_PEA.sub.--2_T15 (SEQ ID NO:23),
HUMTROPIA_PEA.sub.--2_T10(SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 18 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00177 TABLE 18 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 727 741 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 598
612 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 1216 1230 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 1087 1101 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--29 (SEQ ID NO:142)
according to the present invention can be found in the following
transcript(s): HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22),
HUMTROPIA_PEA.sub.--2_T15 (SEQ ID NO:23),
HUMTROPIA_PEA.sub.--2_T3(SEQ ID NO:24) and HUMTROPIA_PEA.sub.--2_T7
(SEQ ID NO:25). Table 19 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00178 TABLE 19 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 742 761 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 613
632 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 1231 1250 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 1102 1121 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--30 (SEQ ID NO:143)
according to the present invention can be found in the following
transcript(s): HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22),
HUMTROPIA_PEA.sub.--2_T15 (SEQ ID NO:23),
HUMTROPIA_PEA.sub.--2_T10(SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 20 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00179 TABLE 20 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 762 774 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 633
645 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 1251 1263 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 1122 1134 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--31 (SEQ ID NO:144)
according to the present invention can be found in the following
transcript(s): HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22),
HUMTROPIA_PEA.sub.--2_T15 (SEQ ID NO:23),
HUMTROPIA_PEA.sub.--2_T3(SEQ ID NO:24) and HUMTROPIA_PEA.sub.--2_T7
(SEQ ID NO:25). Table 21 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00180 TABLE 21 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 775 798 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 646
669 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 1264 1287 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 1135 1158 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--32 (SEQ ID NO:145)
according to the present invention is supported by 40 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T15
(SEQ ID NO:23), HUMTROPIA_PEA.sub.--2.sub.13 T3 (SEQ ID NO:24) and
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table 22 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00181 TABLE 22 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 799 892 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 670
763 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 1288 1381 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 1159 1252 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--4 (SEQ ID NO:146)
according to the present invention can be found in the following
transcript(s): HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22),
HUMTROPIA_PEA.sub.--2_T15 (SEQ ID NO:23),
HUMTROPIA_PEA.sub.--2_T3(SEQ ID NO:24) and HUMTROPIA_PEA.sub.--2_T7
(SEQ ID NO:25). Table 23 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00182 TABLE 23 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 159 171 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T15 159
171 (SEQ ID NO: 23) HUMTROPIA_PEA_2_T3 159 171 (SEQ ID NO: 24)
HUMTROPIA_PEA_2_T7 159 171 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--5 (SEQ ID NO:147)
according to the present invention is supported by 6 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22). Table 24 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00183 TABLE 24 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 172 216 (SEQ ID NO: 22)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.--8 (SEQ ID NO:148)
according to the present invention is supported by 27 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T3
(SEQ ID NO:24) and HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table
25 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00184 TABLE 25 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 217 266 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T3 172
221 (SEQ ID NO: 24) HUMTROPIA_PEA_2_T7 172 221 (SEQ ID NO: 25)
Segment cluster HUMTROPIA_PEA.sub.--2_node.sub.13 9 (SEQ ID NO:149)
according to the present invention is supported by 27 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HUMTROPIA_PEA.sub.--2_T10 (SEQ ID NO:22), HUMTROPIA_PEA.sub.--2_T3
(SEQ ID NO:24) and HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25). Table
26 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00185 TABLE 26 Segment location on transcripts Segment
starting Segment ending Transcript name position position
HUMTROPIA_PEA_2_T10 267 300 (SEQ ID NO: 22) HUMTROPIA_PEA_2_T3 222
255 (SEQ ID NO: 24) HUMTROPIA_PEA_2_T7 222 255 (SEQ ID NO: 25)
Variant Protein Alignment to the Previously Known Protein: Sequence
name: /tmp/p5CHmauP3/NVyK804uFt:TRIC.sub.HUMAN (SEQ ID NO:351)
Sequence documentation: Alignment of:
HUMTROPIA.sub.--PEA.sub.--2_P5 (SEQ ID NO:301) .times.TRIC_HUMAN
(SEQ ID NO:351)
TABLE-US-00186 Alignment segment 1/1: Quality: 1183.00 Escore: 0
Matching length: 124 Total length: 124 Matching Percent Similarity:
100.00 Matching Percent 99.19 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 99.19 Gaps: 0
Alignment:
##STR00027## Sequence name:
/tmp/gCDnOSmn31/GzfEmz5N5Z:TRIC.sub.--HUMAN (SEQ ID NO:351)
Sequence documentation: Alignment of:
HUMTROPIA.sub.--PEA.sub.--2_P12 (SEQ ID NO:302) .times.TRIC_HUMAN
(SEQ ID NO:351)
TABLE-US-00187 Alignment segment 1/1: Alignment: Quality: 873.00
Length: 209 Ratio: 4.823 Gaps: 1 Percent Similarity: 86.603 Percent
Identity: 86.603
alignment_block: HUMTROPIA_PEA.sub.--2_P12 (SEQ ID NO:302)
.times.Troponin Align seg 1/1 to: Troponin from: 1 to: 209
##STR00028## Sequence name:
/tmp/o8saIrMOll/UU1NosjzB3:TRIC.sub.HUMAN (SEQ ID NO:351) Sequence
documentation: Alignment of: HUMTROPIA.sub.--PEA.sub.--2_P17 (SEQ
ID NO:303) .times.TRIC_HUMAN (SEQ ID NO:351)
TABLE-US-00188 Alignment segment 1/1: Quality: 344.00 Escore: 0
Matching length: 35 Total length: 35 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00029## Sequence name:
/tmp/shMGxspSCh/hLCzvaP2j:TRIC.sub.HUMAN (SEQ ID NO:351) Sequence
documentation: Alignment of: HUMTROPIA.sub.--PEA.sub.--2_P18 (SEQ
ID NO:304) .times.TRIC_HUMAN (SEQ ID NO:351)
TABLE-US-00189 Alignment segment 1/1: Quality: 71.00 Escore: 0
Matching length: 9 Total length: 9 Matching Percent Similarity:
88.89 Matching Percent 88.89 Identity: Total Percent Similarity:
88.89 Total Percent Identity: 88.89 Gaps: 0
Alignment:
##STR00030##
Expression of TRIC_HUMAN Troponin I, Cardiac Muscle HUMTROPIA
Transcripts which are Detectable by Amplicon as Depicted in
Sequence Name HUMTROPIA seg10 Specifically in Heart Tissue
Expression of TRIC_HUMAN Troponin I, cardiac muscle transcripts
detectable by or according to seg10 node(s), HUMTROPIA seg10
amplicon(s) (SEQ ID NO:379) and HUMTROPIA seg10F2 (SEQ ID NO:377)
and HUMTROPIA seg10R2 (SEQ ID NO:378) primers was measured by real
time PCR. In parallel the expression of four housekeeping
genes--Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:445);
amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA (GenBank
Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)), RPL19 (GenBank Accession
No. NM.sub.--000981 (SEQ ID NO:437); RPL19 amplicon (SEQ ID
NO:440)), TATA box (GenBank Accession No. NM.sub.--003194 (SEQ ID
NO:441); TATA amplicon (SEQ ID NO:444)) was measured similarly. For
each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the median of the quantities of the heart samples
(Sample Nos. 44-46, Table 1, above "Tissue samples in testing
panel"), to obtain a value of fold up-regulation for each sample
relative to median of the heart.
FIG. 21A is a histogram showing specific expression of the
above-indicated TRIC_HUMAN Troponin I, cardiac muscle transcripts
in heart tissue samples as opposed to other tissues.
As is evident from FIG. 21A, the expression of TRIC_HUMAN Troponin
I, cardiac muscle transcripts detectable by the above amplicon(s)
in heart tissue samples was significantly higher than in most other
samples (non-heart tissue sample Nos. 1-9, 11-26, 28-43, 47-74
Table 1 above "Tissue samples in testing panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: HUMTROPIA seg10F2 forward
primer (SEQ ID NO:377); and HUMTROPIA seg10R2 reverse primer (SEQ
ID NO:378).
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
HUMTROPIA seg10 (SEQ ID NO:379).
TABLE-US-00190 HUMTROPIA seg1 Forward primer (SEQ ID NO:377):
TTGCAGAGGGTCATGCTCG HUMTROPIA seg1 Reverse primer (SEQ ID NO:378):
TCCTTTGGATAGGCACTTCCC HUMTROPIA seg1 Amplicon (SEQ ID NO:379):
TTGCAGAGGGTCATGCTCGGATTGGTGACAGCAGCCTGCGGGCGGAACT
CCGTTGCCCTCGGACTTGCTTAGGGATAGATGGGAAGTGCCTATCCAAA GGA
Expression TRIC_HUMAN Troponin I, Cardiac Muscle HUMTROPIA
Transcripts, which are Detectable by Amplicon as Depicted in
Sequence Name HUMTROPIA seg22 Specifically in Heart Tissue
Expression of TRIC_HUMAN Troponin I, cardiac muscle transcripts
detectable by or according to seg22 node(s), HUMTROPIA seg22
amplicon(s) (SEQ ID NO:382) and HUMTROPIA seg22F (SEQ ID NO:380)
and HUMTROPIA seg22R (SEQ ID NO:381) primers was measured by real
time PCR. In parallel the expression of four housekeeping
genes--RPL19 (GenBank Accession No. NM.sub.--000981 (SEQ ID
NO:437); RPL19 amplicon (SEQ ID NO:440)), TATA box (GenBank
Accession No. NM.sub.--003194 (SEQ ID NO:441); TATA amplicon (SEQ
ID NO:444)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID
NO:445); amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA
(GenBank Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)), was measured similarly.
For each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the median of the quantities of the heart samples
(Sample Nos. 44-46, Table 1, above, "Tissue samples in testing
panel"), to obtain a value of fold up-regulation for each sample
relative to median of the heart.
FIG. 21B is a histogram showing specific expression of the
above-indicated TRIC_HUMAN Troponin I, cardiac muscle transcripts
in heart tissue samples as opposed to other tissues. As is evident
from FIG. 21B, the expression of TRIC_HUMAN Troponin I, cardiac
muscle transcripts detectable by the above amplicon(s) in heart
tissue samples was significantly higher than in the other samples
(non-heart tissue sample Nos. 1-43, 47-74 Table 1 above, "Tissue
samples in testing panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: HUMTROPIA seg22F forward
(SEQ ID NO:380) primer; and HUMTROPIA seg22R (SEQ ID NO:381)
reverse primer.
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
HUMTROPIA seg22 (SEQ ID NO:382).
TABLE-US-00191 HUMTROPIA seg22 Forward primer (SEQ ID NO:380):
GTGGGACGCATGGGCA HUMTROPIA seg22 Reverse primer (SEQ ID NO:381):
TTGTCCTGGGTCTCCTGGG HUMTROPIA seg22 Amplicon (SEQ ID NO:382):
GTGGGACGCATGGGCAGCTCGGGTACCTTCGGGGTAGGGTGAGATGGCTG
GGACTTGGTCTCTGCCTGACCCCTTGCAGCTGCTTTTGGCTGCACATCCC
AGGAGACCCAGGACAA
Expression of TRIC_HUMAN Troponin I, Cardiac Muscle HUMTROPIA
Transcripts which are Detectable by Amplicon as Depicted in
Sequence Name HUMTROPIA seg23-24-25 (SEQ ID NO:384) Specifically in
Heart Tissue
Expression of TRIC_HUMAN Troponin I, cardiac muscle transcripts
detectable by or according to seg23-24-25 node(s), HUMTROPIA
seg23-24-25 amplicon(s) and primers HUMTROPIA seg23-24-25F (SEQ ID
NO:383) and HUMTROPIA seg23-24-25R (SEQ ID NO:384) was measured by
real time PCR. This transcript relates to the known or WT protein
(SEQ ID NO:351). In parallel the expression of four housekeeping
genes--RPL19 (GenBank Accession No. NM.sub.--000981 (SEQ ID
NO:437); RPL19 amplicon (SEQ ID NO:440)), TATA box (GenBank
Accession No. NM.sub.--003194 (SEQ ID NO:441); TATA amplicon (SEQ
ID NO:444)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID
NO:445); amplicon--Ubiquitin-amplicon (SEQ ID NO:448)) and SDHA
(GenBank Accession No. NM.sub.--004168 (SEQ ID NO:449);
amplicon--SDHA-amplicon (SEQ ID NO:452)) was measured similarly.
For each RT sample, the expression of the above amplicons was
normalized to the geometric mean of the quantities of the
housekeeping genes. The normalized quantity of each RT sample was
then divided by the median of the quantities of the heart samples
(Sample Nos. 44-46 Table 1, above), to obtain a value of relative
expression for each sample relative to median of the heart
samples.
FIG. 22 is a histogram showing relative expression of the
above-indicated TRIC_HUMAN Troponin I, cardiac muscle transcripts
in heart tissue samples as opposed to other tissues.
As is evident from FIG. 22, the expression of TRIC_HUMAN Troponin
I, cardiac muscle transcripts detectable by the above amplicon(s)
in heart tissue samples was significantly higher than in the other
samples (Sample Nos. 44-46 Table 1, "Tissue samples in testing
panel").
Primer pairs are also optionally and preferably encompassed within
the present invention; for example, for the above experiment, the
following primer pair was used as a non-limiting illustrative
example only of a suitable primer pair: HUMTROPIA seg23-24-25F (SEQ
ID NO:383) forward primer; and HUMTROPIA seg23-24-25FR (SEQ ID
NO:384) reverse primer.
The present invention also preferably encompasses any amplicon
obtained through the use of any suitable primer pair; for example,
for the above experiment, the following amplicon was obtained as a
non-limiting illustrative example only of a suitable amplicon:
HUMTROPIA seg23-24-25 (SEQ ID NO:384).
TABLE-US-00192 Forward primer HUMTROPIA seg23-24-25F (SEQ ID
NO:383): AAGATCTTTGACCTTCGAGGCA Reverse primer HUMTROPIA
seg23-24-25R (SEQ ID NO:384): CTGCTTGAGGTGGGCCC Amplicon HUMTROPIA
seg23-24-25 (SEQ ID NO:385):
AAGATCTTTGACCTTCGAGGCAAGTTTAAGCGGCCCACCCTGCGGAGAGT
GAGGATCTCTGCAGATGCCATGATGCAGGCGCTGCTGGGGGCCCGGGCTA
AGGAGTCCCTGGACCTGCGGGCCCACCTCAAGCAG
Additional Information--Variant ORFs
With regard to the variants of this cluster, the following should
be noted. Sequence T7 (also referred to herein as
HUMTROPIA_PEA.sub.--2_T7 (SEQ ID NO:25) and troponin T7) has three
open reading frames (ORFs) which are described in greater detail
below.
The sequence in SEQ ID NO: 354 shows CDS-1 frame 1 from 148 to 406
length 259 (bp)=86 (aa) (similar to Troponin I N-ter)
TABLE-US-00193 MADGSSDAAREPRPAPAPIRRRSSNYRAYATEPHAKVGRGFLGAEYRRRR
DPRPWEWGEEPGLRRGRGLRGGASGAEFCRGSCSDW*
The sequence in SEQ ID NO: 355 shows CDS-2 frame 1 from 628 to 1183
length 556 (bp)=185 (aa) (similar to Troponin I C-terminal
portion)
TABLE-US-00194 MILPCSISPWQKKSKISASRKLQLKTLLLQIAKQELEREAEERRGEKGRA
LSTRCQPLELAGLGFAELQDLCRQLHARVDKVDEERYDIEAKVTKNITEI
ADLTQKIFDLRGKFKRPTLRRVRISADAMMQALLGARAKESLDLRAHLKQ
VKKEDTEKENREVGDWRKNIDALSGMEGRKKKFES*
The sequence in SEQ ID NO: 356 shows CDS-3 frame 2 from 155 to 629
length 475 (bp) 158 (aa) (Not similar to Troponin I)
TABLE-US-00195 MGAAMRLGNLALHQPQSDAAPPTTALMPRSRTPRWDGASWGQSTGAGGIQ
DPGSGGRSQGCEGGGDYAEGLQGRSFAEGHARIGDSSLRAELRCPRTCLG
IDGKCLSKGRDPDWWMGMRGVASRRLRAQVGRGPKSGPAGFAGGVLRSPP PSSPNPPP*
However, the presence of three ORFs could potentially complicate
expression and also determination of expression of the desired
protein. The first ORF starts at +1 of Troponin sequence (first
"ATG" is +1 to +3), and the second ORF starts at +8, encoding a 158
amino acid protein. Since the 2nd ATG is located very close to the
first one, there is a possibility that it will be expressed as
well.
In order to eliminate this possibility of expression of the long
ORF, it is possible to optionally introduce two mutations (shown
with regard to FIG. 33):
1. "c" at position 57 to "a"
2. "g" at position 111 to "a"
Both mutations are silent, so the protein sequence will not
change.
Cloning and expression verification of a Troponin variant
HUMTROPIA_PEA.sub.--2 T7 was performed as follows.
1. Full Length Validation
1.1. RNA Preparation
Human adult normal heart RNA pool (lot#A411077) was obtained from
BioChain Inst. Inc. (Hayward, Calif dot 94545 USA dot biochain dot
com). Total RNA samples were treated with DNaseI (Ambion Cat
#1906).
1.2. RT PCR
Purified RNA (1 ug) was mixed with 150 ng Random Hexamer primers
(Invitrogen Cat # 48190-011) and 500 uM dNTP (Takara, Cat #
B9501-1) in a total volume of 15.6 ul DEPC-H2O (Beit Haemek, Cat #
01-852-1A). The mixture was incubated for 5 min at 65.degree. C.
and then quickly chilled on ice. Thereafter, 5 ul of 5.times.
SuperscriptII first strand buffer (Invitrogen, Cat # Y00146), 2.4
ul 0.1M DTT (Invitrogen, Cat #Y00147) and 40 units RNasin (Promega,
Cat # N251A) were added, and the mixture was incubated for 2 min at
42.degree. C. Then, 1 ul (200 units) of SuperscriptII (Invitrogen,
Cat #18064-022) was added and the reaction was incubated for 50 min
at 42.degree. C. and then inactivated at 70.degree. C. for 15 min.
The resulting cDNA was diluted 1:20 in TE buffer (10 mM Tris pH=8,
1 mM EDTA pH=8).
1.3. RT-PCR Analysis
cDNA (5 ul), prepared as described above, was used as a template in
PCR reactions. The amplification was done using AccuPower PCR
PreMix (Bioneer, Korea, Cat# K2016), under the following
conditions: 1 ul--of each primer (10 uM)
TABLE-US-00196 Tropfor CCCTCACTGACCCTCCAAAC (SEQ ID NO: 357)
TropRev CTTCCCATCTATCCCTAAGC (SEQ ID NO: 358)
plus 13 ul --H2O were added into AccuPower PCR PreMix tube with a
reaction program of 5 minutes at 94.degree. C.; 29 cycles of: [30
seconds at 94.degree. C., 30 seconds at 52.degree. C., 40 seconds
at 72.degree. C.] and 10 minutes at 72.degree. C. At the end of the
PCR amplification, products were analyzed on agarose gels stained
with ethidium bromide and visualized with UV light. PCR product was
extracted from the gel using QiaQuick.TM. gel extraction kit
(Qiagen.TM., Cat #28706). The extracted DNA product then served as
a template for secondary PCR reaction under the following
conditions. 5 ul--Amplification .times.10 buffer (Invitrogen Cat #
11708021); 10 ul--purified DNA; 1 ul--dNTPs (10 mM each); 1 ul
MgSO4 (50 mM) 5 .mu.l enhancer solution (Invitrogen, Cat #
11708021); 1 ul--of each primer (10 uM); 26 ul--H.sub.2O and 1.25
units of Taq polymerase [Platinum Pfx DNA polymerase (Invitrogen,
Cat#11708021)] in a total reaction volume of 50 ul. Amplification
was performed with an initial denaturation step at 94.degree. C.
for 3 minutes followed by 29 cycles of [94.degree. C. for 30
seconds, 55.degree. C. for 30 seconds, 68.degree. C. for 40
seconds] and 10 minutes at 68.degree. C. At the end of the PCR
amplification, products were analyzed on agarose gels stained with
ethidium bromide and visualized with UV light. PCR product was
extracted from gel using QiaQuick.TM. gel extraction kit. The
extracted DNA product (FIG. 34) was sequenced by direct sequencing
using the gene specific primers from above (Hy-Labs, Israel),
resulting in the expected sequence of Troponin variant (FIG.
35).
It was concluded that the predicted Troponin variant is indeed a
naturally expressed variant in a normal human tissue as shown in
FIG. 34.
2. Cloning of Troponin Variant into Bacterial Expression Vector
The Troponin splice variant coding sequence was prepared for
cloning by PCR amplification using the fragment described above as
template and Platinum Pfx DNA polymerase (Invitrogen Cat #
11708021) under the following conditions: 5 .mu.l--Amplification
.times.10 buffer (Invitrogen Cat # 11708021); 2 .mu.l--PCR product
from above; 1 .mu.l--dNTPs (10 mM each); 1 .mu.l MgSO4 (50 mM) 5
.mu.l enhancer solution (Invitrogen Cat # 11708021); 33
.mu.l--H.sub.2O; 1 .mu.l--of each primer (10 .mu.M) and 1.25 units
of Taq polymerase [Platinum Pfx DNA polymerase (Invitrogen Cat #
11708021)] in a total reaction volume of 50 .mu.l with a reaction
program of 3 minutes at 94.degree. C.; 29 cycles of: [30 seconds at
94.degree. C., 30 seconds at 58.degree. C., 40 seconds at
68.degree. C.] and 7 minutes at 68.degree. C. The Primers listed
below include specific sequences of the nucleotide sequence
corresponding to the splice variant and NheI and HindIII
restriction sites.
TABLE-US-00197 (SEQ ID NO: 359) Trop
NheIfor-ACAGCTAGCATGGCGGATGGGAGCAGC (SEQ ID NO: 360)
TropHindIIIrev-CCTAAGCTTCACCAATCCGAGCATGAC
The PCR product was then double digested with NheI and HindIII (New
England Biolabs (UK) LTD), and inserted into pRSET-A (Invitrogen,
Cat# V351-20), previously digested with the same enzymes, in-frame
to an N-terminal 6His-tag, to give HisTroponin T7 pRSET (FIG. 36;
(SEQ ID NO:386)). The coding sequence encodes for a protein having
the 6His-tag at the N' end (6His residues in a row at one end of
the protein), and 8 additional amino acids encoded by the pRSET
vector.
The sequence of the Troponin insert in the final plasmid, as well
as its flanking regions, were verified by sequencing and found to
be identical to the desired sequences. The complete sequence of His
Troponin T7 pRESTA is shown in FIG. 37 (SEQ ID NO:386).
FIG. 38 shows the translated sequence of Troponin variant with the
location of the His-tag marked (SEQ ID NO:387).
3. Bacterial Cell Growth and Induction of Protein Expression
HisTroponin pRSETA DNA was transformed into competent BL21 Gold
cells (Stratagene Cat#230134). Ampicillin resistant transformants
were screened and positive clones were further analyzed by
restriction enzyme digestion and sequence verification.
Cells containing the HisTroponin T7 pRSET vector or empty pRSET
vector (as negative control) were grown in LB medium, supplemented
with Ampicillin (50 .mu.g/ml) and chloramphenicol (34 .mu.g/ml).
Cells were grown until O.D..sub.600 nm reaches 0.5. This value was
reached in about 3 hours. 1 mM IPTG (Roche, Cat #724815) was added
and the cells were grown at 37.degree. C. for additional 3 hours. 1
ml of each culture was removed for gel analysis at T.sub.0 and
T.sub.3.
3.1. Coomassie Staining and Western Blotting Results
The time course of small-scale expression of Troponin in BL21Gold
is demonstrated in FIG. 39a-b. The expression of a recombinant
protein with the appropriate molecular weight (11 kDa) was detected
both by Coomassie staining (FIG. 39a) and by Western blot using
anti His-antibodies (BD Clontech, Ref 631212) (FIG. 39b). It was
concluded that the protein encoded by Troponin variant T7 could be
expressed in bacterial cells.
Description for Cluster HUMSMCK
Cluster HUMSMCK features 5 transcript(s) and 14 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00198 TABLE 1 Transcripts of interest Transcript Name Seq
ID No. HUMSMCK_T5 26 HUMSMCK_T6 27 HUMSMCK_T7 28 HUMSMCK_T9 29
HUMSMCK_T11 30
TABLE-US-00199 TABLE 2 Segments of interest Segment Name Seq ID No.
HUMSMCK_node_0 150 HUMSMCK_node_7 151 HUMSMCK_node_12 152
HUMSMCK_node_17 153 HUMSMCK_node_22 154 HUMSMCK_node_23 155
HUMSMCK_node_25 156 HUMSMCK_node_26 157 HUMSMCK_node_28 158
HUMSMCK_node_29 159 HUMSMCK_node_32 160 HUMSMCK_node_11 161
HUMSMCK_node_14 162 HUMSMCK_node_19 163
TABLE-US-00200 TABLE 3 Proteins of interest Protein Name Seq ID No.
Corresponding Transcript(s) HUMSMCK_P4 305 HUMSMCK_T5 (SEQ ID NO:
26) HUMSMCK_P5 306 HUMSMCK_T6 (SEQ ID NO: 27) HUMSMCK_P6 307
HUMSMCK_T7 (SEQ ID NO: 28); HUMSMCK_T11 (SEQ ID NO: 30) HUMSMCK_P8
308 HUMSMCK_T9 (SEQ ID NO: 29)
These sequences are variants of the known protein Creatine kinase,
sarcomeric mitochondrial precursor (SEQ ID NO:388) (SwissProt
accession identifier KCRS_HUMAN; known also according to the
synonyms EC 2.7.3.2; S-MtCK; Mib-CK; Basic-type mitochondrial
creatine kinase), referred to herein as the previously known
protein.
Protein Creatine kinase, sarcomeric mitochondrial precursor (SEQ ID
NO:388) is known or believed to have the following function(s):
Reversibly catalyzes the transfer of phosphate between ATP and
various phosphogens (e.g. creatine phosphate). Creatine kinase
isoenzymes play a central role in energy transduction in tissues
with large, fluctuating energy demands, such as skeletal muscle,
heart, brain and spermatozoa. The sequence for protein Creatine
kinase, sarcomeric mitochondrial precursor is given at the end of
the application, as "Creatine kinase, sarcomeric mitochondrial
precursor amino acid sequence" (SEQ ID NO:388). Known polymorphisms
for this sequence are as shown in Table 4.
TABLE-US-00201 TABLE 4 Amino acid mutations for Known Protein SNP
position(s) on amino acid sequence Comment 74 S -> A
Protein Creatine kinase, sarcomeric mitochondrial precursor (SEQ ID
NO:388) localization is believed to be Mitochondrial inner
membrane; outer side.
The following GO Annotation(s) apply to the previously known
protein. The following annotation(s) were found: energy pathways;
muscle contraction, which are annotation(s) related to Biological
Process; creatine kinase; transferase, transferring
phosphorus-containing groups, which are annotation(s) related to
Molecular Function; and mitochondrion, which are annotation(s)
related to Cellular Component.
The GO assignment relies on information from one or more of the
SwissProt/TremB1 Protein knowledgebase, available from <dot
expasy dot ch/sprot/>; or Locuslink, available from <dot ncbi
dot nlm dot nih dot gov/projects/LocusLink/>.
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster HUMSMCK. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 23 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 23, concerning the number of
heart-specific clones in libraries/sequences; as well as with
regard to the histogram in FIG. 24, concerning the actual
expression of oligonucleotides in various tissues, including
heart.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs, which was found to be 18.1; the ratio of
expression of the cluster in heart specific ESTs to the overall
expression of the cluster in muscle-specific ESTs which was found
to be 2.4; and fisher exact test P-values were computed both for
library and weighted clone counts to check that the counts are
statistically significant, and were found to be 3.60E-23.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the ratio of expression of the cluster
in heart specific ESTs to the overall expression of the cluster in
muscle-specific ESTs which was found to be 18.1, which clearly
supports specific expression in heart tissue.
As noted above, cluster HUMSMCK features 5 transcript(s), which
were listed in Table 1 above. These transcript(s) encode for
protein(s) which are variant(s) of protein Creatine kinase,
sarcomeric mitochondrial precursor (SEQ ID NO:388). A description
of each variant protein according to the present invention is now
provided.
Variant protein HUMSMCK_P4 (SEQ ID NO:305) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) HUMSMCK_T5 (SEQ ID
NO:26). An alignment is given to the known protein (Creatine
kinase, sarcomeric mitochondrial precursor (SEQ ID NO:388)) at the
end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between HUMSMCK_P4 (SEQ ID NO:305) and
KCRS_HUMAN_V1 (SEQ ID NO:347):
1. An isolated chimeric polypeptide encoding for HUMSMCK_P4 (SEQ ID
NO:305), comprising a first amino acid sequence being at least 90%
homologous to
MASIFSKLLTGRNASLLFATMGTSVLTTGYLLNRQKVCAEVREQPRLFPPSADYPDLRK
HNNCMAECLTPAIYAKLRNKVTPNGYTLDQCIQTGVDNPGHPFIKTVGMVAGDEESYE
VFADLFDPVIKLRHNGYDPRVMKHTTDLDASKITQGQFDEHYVLSSRVRTGRSIRGLSL
PPACTRAERREVENVAITALEGLKGDLAGRYYKLSEMTEQDQQRLIDDHFLFDKPVSPL
LTCAGMARDWPDARGIWHNYDKTFLIWINEEDHTRVISMEKGGNMKRVFERFCRGLK
EVERLIQERGWEFMWNERLGYILTCPSNLGTGLRAGVHVRIPKLSKDPRFSKILENLRLQ
KRGTGGVDTAAVADVYDISNIDRIGRSEV corresponding to amino acids 1-381 of
KCRS_HUMAN_V1 (SEQ ID NO:347), which also corresponds to amino
acids 1-381 of HUMSMCK_P4 (SEQ ID NO:305), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence TSLSLS
(SEQ ID NO:415) corresponding to amino acids 382-387 of HUMSMCK_P4
(SEQ ID NO:305), wherein said first amino acid sequence and second
amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of HUMSMCK_P4 (SEQ
ID NO:305), comprising a polypeptide being at least 70%, optionally
at least about 80%, preferably at least about 85%, more preferably
at least about 90% and most preferably at least about 95%
homologous to the sequence TSLSLS (SEQ ID NO:415) in HUMSMCK_P4
(SEQ ID NO:305).
It should be noted that the known protein sequence (KCRS_HUMAN; SEQ
ID NO:388) has one or more changes than the sequence given at the
end of the application and named as being the amino acid sequence
for KCRS_HUMAN_V1 (SEQ ID NO:347). These changes were previously
known to occur and are listed in the table below.
TABLE-US-00202 TABLE 5 Changes to KCRS_HUMAN_V1 (SEQ ID NO: 347)
SNP position(s) on amino acid sequence Type of change 75
conflict
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because of manual inspection of known protein
localization and/or gene structure.
Variant protein HUMSMCK_P4 (SEQ ID NO:305) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 6, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein HUMSMCK_P4 (SEQ ID NO:305) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00203 TABLE 6 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
59 K -> No 60 H -> No 74 A -> S Yes 117 E -> * No 117 E
-> No 249 R -> No
Variant protein HUMSMCK_P4 (SEQ ID NO:305) is encoded by the
following transcript(s): HUMSMCK_T5 (SEQ ID NO:26), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript HUMSMCK_T5 (SEQ ID NO:26) is shown in bold;
this coding portion starts at position 1305 and ends at position
2465. The transcript also has the following SNPs as listed in Table
7 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein HUMSMCK_P4 (SEQ ID NO:305) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00204 TABLE 7 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> C Yes 545 G -> T Yes 1481 G -> No 1482 C -> No
1524 G -> T Yes 1653 G -> No 1653 G -> T No 2050 G ->
No 2228 T -> C No 2231 G -> A No 2489 C -> T Yes
Variant protein HUMSMCK_P5 (SEQ ID NO:306) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) HUMSMCK_T6 (SEQ ID
NO:27). An alignment is given to the known protein (Creatine
kinase, sarcomeric mitochondrial precursor (SEQ ID NO:388)) at the
end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between HUMSMCK_P5 (SEQ ID NO:306) and
KCRS_HUMAN_V1 (SEQ ID NO:347):
1. An isolated chimeric polypeptide encoding for HUMSMCK_P5 (SEQ ID
NO:306), comprising a first amino acid sequence being at least 90%
homologous to
MASIFSKLLTGRNASLLFATMGTSVLTTGYLLNRQKVCAEVREQPRLFPPSADYPDLRK
HNNCMAECLTPAIYAKLRNKVTPNGYTLDQCIQTGVDNPGHPFIKTVGMVAGDEESYE
VFADLFDPVIKLRHNGYDPRVMKHTTDLDASKITQGQFDEHYVLSSRVRTGRSIRGLSL
PPACTRAERREVENVAITALEGLKGDLAGRYYKLSEMTEQDQQRLIDDHFLFDKPVSPL
LTCAGMARDWPDARGIWHNYDKTFLIWINEEDHTRVISMEKGGNMKRVFERFCRGLK
EVERLIQERGWEFMWNERLGYILTCPSNLGTGLRAGVHVRIPKLSK corresponding to
amino acids 1-338 of KCRS_HUMAN_V1 (SEQ ID NO:347), which also
corresponds to amino acids 1-338 of HUMSMCK_P5 (SEQ ID NO:306), and
a second amino acid sequence being at least 70%, optionally at
least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide having
the sequence VLLCAQWP (SEQ ID NO:416) corresponding to amino acids
339-346 of HUMSMCK_P5 (SEQ ID NO:306), wherein said first amino
acid sequence and second amino acid sequence are contiguous and in
a sequential order.
2. An isolated polypeptide encoding for a tail of HUMSMCK_P5 (SEQ
ID NO:306), comprising a polypeptide being at least 70%, optionally
at least about 80%, preferably at least about 85%, more preferably
at least about 90% and most preferably at least about 95%
homologous to the sequence VLLCAQWP (SEQ ID NO:416) in HUMSMCK_P5
(SEQ ID NO:306).
It should be noted that the known protein sequence (KCRS_HUMAN (SEQ
ID NO:388)) has one or more changes than the sequence given at the
end of the application and named as being the amino acid sequence
for KCRS_HUMAN_V1 (SEQ ID NO:347). These changes were previously
known to occur and are listed in the table below.
TABLE-US-00205 TABLE 8 Changes to KCRS_HUMAN_V1 (SEQ ID NO: 347)
SNP position(s) on amino acid sequence Type of change 75
Conflict
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because of manual inspection of known protein
localization and/or gene structure.
Variant protein HUMSMCK_P5 (SEQ ID NO:306) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 9, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein HUMSMCK_P5 (SEQ ID NO:306) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00206 TABLE 9 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
59 K -> No 60 H -> No 74 A -> S Yes 117 E -> * No 117 E
-> No 249 R -> No
Variant protein HUMSMCK_P5 (SEQ ID NO:306) is encoded by the
following transcript(s): HUMSMCK_T6 (SEQ ID NO:27), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript HUMSMCK_T6 (SEQ ID NO:27) is shown in bold;
this coding portion starts at position 1305 and ends at position
2342. The transcript also has the following SNPs as listed in Table
10 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein HUMSMCK_P5 (SEQ ID NO:306) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00207 TABLE 10 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> C Yes 545 G -> T Yes 1481 G -> No 1482 C -> No
1524 G -> T Yes 1653 G -> No 1653 G -> T No 2050 G ->
No 2228 T -> C No 2231 G -> A No
Variant protein HUMSMCK_P6 (SEQ ID NO:307) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) HUMSMCK_T7 (SEQ ID
NO:28) and HUMSMCK_T1 (SEQ ID NO:30). An alignment is given to the
known protein (Creatine kinase, sarcomeric mitochondrial precursor
(SEQ ID NO:388)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HUMSMCK_P6 (SEQ ID NO:307) and
KCRS_HUMAN_V1 (SEQ ID NO:347):
1. An isolated chimeric polypeptide encoding for HUMSMCK_P6 (SEQ ID
NO:307), comprising a first amino acid sequence being at least 90%
homologous to
MASIFSKLLTGRNASLLFATMGTSVLTTGYLLNRQKVCAEVREQPRLFPPSADYPDLRK
HNNCMAECLTPAIYAKLRNKVTPNGYTLDQCIQTGVDNPGHPFIKTVGMVAGDEESYE
VFADLFDPVIKLRHNGYDPRVMKHTTDLDASKITQGQFDEHYVLSSRVRTGRSIRGLSL
PPACTRAERREVENVAITALEGLKGDLAGRYYKLSEMTEQDQQRLID corresponding to
amino acids 1-223 of KCRS_HUMAN_V1 (SEQ ID NO:347), which also
corresponds to amino acids 1-223 of HUMSMCK_P6 (SEQ ID NO:307), and
a second amino acid sequence being at least 70%, optionally at
least 80%, preferably at least 85%, more preferably at least 90%
and most preferably at least 95% homologous to a polypeptide having
the sequence A corresponding to amino acids 224-224 of HUMSMCK_P6
(SEQ ID NO:307), wherein said first amino acid sequence and second
amino acid sequence are contiguous and in a sequential order.
It should be noted that the known protein sequence (KCRS_HUMAN (SEQ
ID NO:388)) has one or more changes than the sequence given at the
end of the application and named as being the amino acid sequence
for KCRS_HUMAN_V1 (SEQ ID NO:347). These changes were previously
known to occur and are listed in the table below.
TABLE-US-00208 TABLE 11 Changes to KCRS_HUMAN_V1 (SEQ ID NO: 347)
SNP position(s) on amino acid sequence Type of change 75
Conflict
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because of manual inspection of known protein
localization and/or gene structure.
Variant protein HUMSMCK_P6 (SEQ ID NO:307) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 12, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein HUMSMCK_P6 (SEQ ID NO:307) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00209 TABLE 12 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
59 K -> No 60 H -> No 74 A -> S Yes 117 E -> * No 117 E
-> No
Variant protein HUMSMCK_P6 (SEQ ID NO:307) is encoded by the
following transcript(s): HUMSMCK_T7 (SEQ ID NO:28) and HUMSMCK_T11
(SEQ ID NO:30), for which the sequence(s) is/are given at the end
of the application.
The coding portion of transcript HUMSMCK_T7 (SEQ ID NO:28) is shown
in bold; this coding portion starts at position 1305 and ends at
position 1976. The transcript also has the following SNPs as listed
in Table 13 (given according to their position on the nucleotide
sequence, with the alternative nucleic acid listed; the last column
indicates whether the SNP is known or not; the presence of known
SNPs in variant protein HUMSMCK_P6 (SEQ ID NO:307) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00210 TABLE 13 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> C Yes 545 G -> T Yes 1481 G -> No 1482 C -> No
1524 G -> T Yes 1653 G -> No 1653 G -> T No 2142 T -> C
No 2145 G -> A No 2398 C -> A Yes 2521 G -> A Yes
The coding portion of transcript HUMSMCK_T11 (SEQ ID NO:30) is
shown in bold; this coding portion starts at position 1305 and ends
at position 1976. The transcript also has the following SNPs as
listed in Table 14 (given according to their position on the
nucleotide sequence, with the alternative nucleic acid listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein HUMSMCK_P6 (SEQ ID NO:307)
sequence provides support for the deduced sequence of this variant
protein according to the present invention).
TABLE-US-00211 TABLE 14 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> C Yes 545 G -> T Yes 1481 G -> No 1482 C -> No
1524 G -> T Yes 1653 G -> No 1653 G -> T No
Variant protein HUMSMCK_P8 (SEQ ID NO:308) according to the present
invention has an amino acid sequence as given at the end of the
application; it is encoded by transcript(s) HUMSMCK_T9 (SEQ ID
NO:29). An alignment is given to the known protein (Creatine
kinase, sarcomeric mitochondrial precursor (SEQ ID NO:388)) at the
end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between HUMSMCK_P8 (SEQ ID NO:308) and
KCRS_HUMAN_V1 (SEQ ID NO:347):
1. An isolated chimeric polypeptide encoding for HUMSMCK_P8 (SEQ ID
NO:308), comprising a first amino acid sequence being at least 90%
homologous to
MASIFSKLLTGRNASLLFATMGTSVLTTGYLLNRQKVCAEVREQPRLFPPSADYPDLRK
HNNCMAECLTPAIYAKLRNKVTPNGYTLDQCIQTGVDNPGHPFIKTVGMVAGDEESYE
VFADLFDPVIKLRHNGYDPRVMKHTTDLDASKITQGQFDEHYVLSSRVRTGRSIRGLSL
PPACTRAERREVENVAITALEGLKGDLAGRYYKLSEMTEQDQQRLIDDHFLFDKPVSPL
LTCAGMARDWPDARGIWHNYDKTFLIWINEEDHTRVISMEKGGNMKRVFERFCRGLK EV
corresponding to amino acids 1-294 of KCRS_HUMAN_V1 (SEQ ID
NO:347), which also corresponds to amino acids 1-294 of HUMSMCK_P8
(SEQ ID NO:308), and a second amino acid sequence being at least
70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide having the sequence RCYLRFLDIY (SEQ ID NO:417)
corresponding to amino acids 295-304 of HUMSMCK_P8 (SEQ ID NO:308),
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of HUMSMCK_P8 (SEQ
ID NO:308), comprising a polypeptide being at least 70%, optionally
at least about 80%, preferably at least about 85%, more preferably
at least about 90% and most preferably at least about 95%
homologous to the sequence RCYLRFLDIY (SEQ ID NO:417) in HUMSMCK_P8
(SEQ ID NO:308).
It should be noted that the known protein sequence (KCRS_HUMAN (SEQ
ID NO:388)) has one or more changes than the sequence given at the
end of the application and named as being the amino acid sequence
for KCRS_HUMAN_V1 (SEQ ID NO:347). These changes were previously
known to occur and are listed in the table below.
TABLE-US-00212 TABLE 15 Changes to KCRS_HUMAN_V1 (SEQ ID NO: 347)
SNP position(s) on amino acid sequence Type of change 75
Conflict
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellular because of manual inspection of known protein
localization and/or gene structure.
Variant protein HUMSMCK_P8 (SEQ ID NO:308) also has the following
non-silent SNPs (Single Nucleotide Polymorphisms) as listed in
Table 16, (given according to their position(s) on the amino acid
sequence, with the alternative amino acid(s) listed; the last
column indicates whether the SNP is known or not; the presence of
known SNPs in variant protein HUMSMCK_P8 (SEQ ID NO:308) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00213 TABLE 16 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
59 K -> No 60 H -> No 74 A -> S Yes 117 E -> * No 117 E
-> No 249 R -> .sup. No
Variant protein HUMSMCK_P8 (SEQ ID NO:308) is encoded by the
following transcript(s): HUMSMCK_T9 (SEQ ID NO:29), for which the
sequence(s) is/are given at the end of the application. The coding
portion of transcript HUMSMCK_T9 (SEQ ID NO:29) is shown in bold;
this coding portion starts at position 1305 and ends at position
2216. The transcript also has the following SNPs as listed in Table
17 (given according to their position on the nucleotide sequence,
with the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein HUMSMCK_P8 (SEQ ID NO:308) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00214 TABLE 17 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> C Yes 545 G -> T Yes 1481 G -> No 1482 C -> No
1524 G -> T Yes 1653 G -> No 1653 G -> T No 2050 G ->
No
As noted above, cluster HUMSMCK features 14 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster HUMSMCK_node.sub.--0 (SEQ ID NO:150) according to
the present invention is supported by 38 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26),
HUMSMCK_T6 (SEQ ID NO:27), HUMSMCK_T7 (SEQ ID NO:28), HUMSMCK_T9
(SEQ ID NO:29) and HUMSMCK_T11 (SEQ ID NO:30). Table 18 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00215 TABLE 18 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 1 1284 HUMSMCK_T6 (SEQ ID NO: 27) 1 1284
HUMSMCK_T7 (SEQ ID NO: 28) 1 1284 HUMSMCK_T9 (SEQ ID NO: 29) 1 1284
HUMSMCK_T11 (SEQ ID NO: 30) 1 1284
Segment cluster HUMSMCK_node.sub.--7 (SEQ ID NO:151) according to
the present invention is supported by 47 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26),
HUMSMCK_T6 (SEQ ID NO:27), HUMSMCK_T7 (SEQ ID NO:28), HUMSMCK_T9
(SEQ ID NO:29) and HUMSMCK_T11(SEQ ID NO:30). Table 19 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00216 TABLE 19 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 1285 1456 HUMSMCK_T6 (SEQ ID NO: 27)
1285 1456 HUMSMCK_T7 (SEQ ID NO: 28) 1285 1456 HUMSMCK_T9 (SEQ ID
NO: 29) 1285 1456 HUMSMCK_T11 (SEQ ID NO: 30) 1285 1456
Segment cluster HUMSMCK_node.sub.--12 (SEQ ID NO:152) according to
the present invention is supported by 54 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26),
HUMSMCK_T6 (SEQ ID NO:27), HUMSMCK_T7 (SEQ ID NO:28), HUMSMCK_T9
(SEQ ID NO:29) and HUMSMCK_T11 (SEQ ID NO:30). Table 20 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00217 TABLE 20 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 1476 1655 HUMSMCK_T6 (SEQ ID NO: 27)
1476 1655 HUMSMCK_T7 (SEQ ID NO: 28) 1476 1655 HUMSMCK_T9 (SEQ ID
NO: 29) 1476 1655 HUMSMCK_T11 (SEQ ID NO: 30) 1476 1655
Segment cluster HUMSMCK_node.sub.--17 (SEQ ID NO:153) according to
the present invention is supported by 48 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26),
HUMSMCK_T6 (SEQ ID NO:27), HUMSMCK_T7 (SEQ ID NO:28), HUMSMCK_T9
(SEQ ID NO:29) and HUMSMCK_T111 (SEQ ID NO:30). Table 21 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00218 TABLE 21 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 1752 1973 HUMSMCK_T6 (SEQ ID NO: 27)
1752 1973 HUMSMCK_T7 (SEQ ID NO: 28) 1752 1973 HUMSMCK_T9 (SEQ ID
NO: 29) 1752 1973 HUMSMCK_T11 (SEQ ID NO: 30) 1752 1973
Segment cluster HUMSMCK_node.sub.--22 (SEQ ID NO:154) according to
the present invention is supported by 60 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26),
HUMSMCK_T6 (SEQ ID NO:27), HUMSMCK_T7 (SEQ ID NO:28), HUMSMCK_T9
(SEQ ID NO:29) and HUMSMCK_T111 (SEQ ID NO:30). Table 22 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00219 TABLE 22 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 2060 2183 HUMSMCK_T6 (SEQ ID NO: 27)
2060 2183 HUMSMCK_T7 (SEQ ID NO: 28) 1974 2097 HUMSMCK_T9 (SEQ ID
NO: 29) 2060 2183 HUMSMCK_T11 (SEQ ID NO: 30) 1974 2097
Segment cluster HUMSMCK_node.sub.--23 (SEQ ID NO:155) according to
the present invention is supported by 3 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T9 (SEQ ID NO:29)
and HUMSMCK_T11(SEQ ID NO:30). Table 23 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00220 TABLE 23 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T9 (SEQ ID NO: 29) 2184 2382 HUMSMCK_T11 (SEQ ID NO: 30)
2098 2296
Segment cluster HUMSMCK_node.sub.--25 (SEQ ID NO:156) according to
the present invention is supported by 58 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26),
HUMSMCK_T6 (SEQ ID NO:27) and HUMSMCK_T7 (SEQ ID NO:28). Table 24
below describes the starting and ending position of this segment on
each transcript.
TABLE-US-00221 TABLE 24 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 2184 2318 HUMSMCK_T6 (SEQ ID NO: 27)
2184 2318 HUMSMCK_T7 (SEQ ID NO: 28) 2098 2232
Segment cluster HUMSMCK_node.sub.--26 (SEQ ID NO:157) according to
the present invention is supported by 1 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T6 (SEQ ID NO:27).
Table 25 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00222 TABLE 25 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T6 (SEQ ID NO: 27) 2319 2448
Segment cluster HUMSMCK_node.sub.--28 (SEQ ID NO:158) according to
the present invention is supported by 59 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26)
and HUMSMCK_T7 (SEQ ID NO:28). Table 26 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00223 TABLE 26 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 2319 2444 HUMSMCK_T7 (SEQ ID NO: 28)
2233 2358
Segment cluster HUMSMCK_node.sub.--29 (SEQ ID NO:159) according to
the present invention is supported by 3 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26).
Table 27 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00224 TABLE 27 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 2445 2820
Segment cluster HUMSMCK_node.sub.--32 (SEQ ID NO:160) according to
the present invention is supported by 62 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T7 (SEQ ID NO:28).
Table 28 below describes the starting and ending position of this
segment on each transcript.
TABLE-US-00225 TABLE 28 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T7 (SEQ ID NO: 28) 2359 2632
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster HUMSMCK_node.sub.--11 (SEQ ID NO:161) according to
the present invention can be found in the following transcript(s):
HUMSMCK_T5 (SEQ ID NO:26), HUMSMCK_T6 (SEQ ID NO:27), HUMSMCK_T7
(SEQ ID NO:28), HUMSMCK_T9 (SEQ ID NO:29) and HUMSMCK_T11 (SEQ ID
NO:30). Table 29 below describes the starting and ending position
of this segment on each transcript.
TABLE-US-00226 TABLE 29 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 1457 1475 HUMSMCK_T6 (SEQ ID NO: 27)
1457 1475 HUMSMCK_T7 (SEQ ID NO: 28) 1457 1475 HUMSMCK_T9 (SEQ ID
NO: 29) 1457 1475 HUMSMCK_T11 (SEQ ID NO: 30) 1457 1475
Segment cluster HUMSMCK_node.sub.--14 (SEQ ID NO:162) according to
the present invention is supported by 38 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26),
HUMSMCK_T6 (SEQ ID NO:27), HUMSMCK_T7 (SEQ ID NO:28), HUMSMCK_T9
(SEQ ID NO:29) and HUMSMCK_T11 (SEQ ID NO:30). Table 30 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00227 TABLE 30 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 1656 1751 HUMSMCK_T6 (SEQ ID NO: 27)
1656 1751 HUMSMCK_T7 (SEQ ID NO: 28) 1656 1751 HUMSMCK_T9 (SEQ ID
NO: 29) 1656 1751 HUMSMCK_T11 (SEQ ID NO: 30) 1656 1751
Segment cluster HUMSMCK_node.sub.13 19 (SEQ ID NO:163) according to
the present invention is supported by 47 libraries. The number of
libraries was determined as previously described. This segment can
be found in the following transcript(s): HUMSMCK_T5 (SEQ ID NO:26),
HUMSMCK_T6 (SEQ ID NO:27) and HUMSMCK_T9 (SEQ ID NO:29). Table 31
below describes the starting and ending position of this segment on
each transcript.
TABLE-US-00228 TABLE 31 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HUMSMCK_T5 (SEQ ID NO: 26) 1974 2059 HUMSMCK_T6 (SEQ ID NO: 27)
1974 2059 HUMSMCK_T9 (SEQ ID NO: 29) 1974 2059
Variant Protein Alignment to the Previously Known Protein: Sequence
name: KCRS_HUMAN _V1 (SEQ ID NO:347) Sequence documentation:
Alignment of: HUMSMCK_P4 (SEQ ID NO:305) .times.KCRS_HUMAN_V1 (SEQ
ID NO:347)
TABLE-US-00229 Alignment segment 1/1: Quality: 3745.00 Escore: 0
Matching length: 381 Total length: 381 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00031## Sequence mane: KCRS_HUMAN_V1 (SEQ ID NO:347) Sequence
documentation: Alignment of: HUMSMCK_P5 (SEQ ID NO:306)
.times.KCRS_HUMAN_V1 (SEQ ID NO:347)
TABLE-US-00230 Alignment segment 1/1: Quality: 3344.00 Escore: 0
Matching length: 338 Total length: 338 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00032## Sequence name: KCRS_HUMAN _V1 (SEQ ID NO:347) Sequence
documentation: Alignment of: HUMSMCK_P6 (SEQ ID NO:307)
.times.KCRS_HUMAN_V1 (SEQ ID NO:347)
TABLE-US-00231 Alignment segment 1/1: Quality: 2176.00 Escore: 0
Matching length: 223 Total length: 223 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00033## Sequence name: KCRS_HUMAN _V1 (SEQ ID NO:347) Sequence
documentation: Alignment of: HUMSMCK_P8 (SEQ ID NO:308)
.times.KCRS_HUMAN_V1 (SEQ ID NO:347)
TABLE-US-00232 Alignment segment 1/1: Quality: 2904.00 Escore: 0
Matching length: 294 Total length: 294 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment
##STR00034##
Description for Cluster H88495
Cluster H88495 features 7 transcript(s) and 22 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00233 TABLE 1 Transcripts of interest Transcript Name Seq
ID No. H88495_PEA_3_T3 31 H88495_PEA_3_T4 32 H88495_PEA_3_T5 33
H88495_PEA_3_T6 34 H88495_PEA_3_T7 35 H88495_PEA_3_T8 36
H88495_PEA_3_T9 37
TABLE-US-00234 TABLE 2 Segments of interest Segment Name Seq ID No.
H88495_PEA_3_node_0 164 H88495_PEA_3_node_1 165 H88495_PEA_3_node_4
166 H88495_PEA_3_node_9 167 H88495_PEA_3_node_13 168
H88495_PEA_3_node_19 169 H88495_PEA_3_node_21 170
H88495_PEA_3_node_26 171 H88495_PEA_3_node_2 172
H88495_PEA_3_node_5 173 H88495_PEA_3_node_6 174 H88495_PEA_3_node_7
175 H88495_PEA_3_node_8 176 H88495_PEA_3_node_10 177
H88495_PEA_3_node_11 178 H88495_PEA_3_node_12 179
H88495_PEA_3_node_14 180 H88495_PEA_3_node_16 181
H88495_PEA_3_node_18 182 H88495_PEA_3_node_20 183
H88495_PEA_3_node_23 184 H88495_PEA_3_node_24 185
TABLE-US-00235 TABLE 3 Proteins of interest Protein Name Seq ID No.
Corresponding Transcript(s) H88495_PEA_3_P15 309 H88495_PEA_3_T3
(SEQ ID NO: 31); H88495_PEA_3_T4 (SEQ ID NO: 32); H88495_PEA_3_T7
(SEQ ID NO: 35) H88495_PEA_3_P16 310 H88495_PEA_3_T5 (SEQ ID NO:
33); H88495_PEA_3_T6 (SEQ ID NO: 34) H88495_PEA_3_P17 311
H88495_PEA_3_T8 (SEQ ID NO: 36) H88495_PEA_3_P18 312
H88495_PEA_3_T9 (SEQ ID NO: 37)
These sequences are variants of the known protein Sarcoplasmic
reticulum histidine-rich calcium-binding protein precursor (SEQ ID
NO:389) (SwissProt accession identifier SRCH_HUMAN), referred to
herein as the previously known protein.
Protein Sarcoplasmic reticulum histidine-rich calcium-binding
protein precursor (SEQ ID NO:389) is known or believed to have the
following function(s): May play a role in the regulation of calcium
sequestration or release in the SR of skeletal and cardiac muscle.
The sequence for protein Sarcoplasmic reticulum histidine-rich
calcium-binding protein precursor is given at the end of the
application, as "Sarcoplasmic reticulum histidine-rich
calcium-binding protein precursor amino acid sequence" (SEQ ID
NO:389). Known polymorphisms for this sequence are as shown in
Table 4.
TABLE-US-00236 TABLE 4 Amino acid mutations for Known Protein SNP
position(s) on amino acid sequence Comment 96 S -> A.
/FTId=VAR_005623. 204 Missing. /FTId=VAR_011622.
Protein Sarcoplasmic reticulum histidine-rich calcium-binding
protein precursor (SEQ ID NO:389) localization is believed to be
Sarcoplasmic reticulum lumen.
The following GO Annotation(s) apply to the previously known
protein. The following annotation(s) were found: muscle
contraction, which are annotation(s) related to Biological Process;
and calcium binding, which are annotation(s) related to Molecular
Function.
The GO assignment relies on information from one or more of the
SwissProt/TremB1 Protein knowledgebase, available from <dot
expasy dot ch/sprot/>; or Locuslink, available from <dot ncbi
dot nlm dot nih dot gov/projects/LocusLink/>.
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster H88495. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 25 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 25, concerning the number of
heart-specific clones in libraries/sequences; as well as with
regard to the histogram in FIG. 26, concerning the actual
expression of oligonucleotides in various tissues, including
heart.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs, which was found to be 13.7; the ratio of
expression of the cluster in heart specific ESTs to the overall
expression of the cluster in muscle-specific ESTs which was found
to be 2.3; and fisher exact test P-values were computed both for
library and weighted clone counts to check that the counts are
statistically significant, and were found to be 1.90E-06.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the ratio of expression of the cluster
in heart specific ESTs to the overall expression of the cluster in
muscle-specific ESTs which was found to be 13.7, which clearly
supports specific expression in heart tissue.
As noted above, cluster H88495 features 7 transcript(s), which were
listed in Table 1 above. These transcript(s) encode for protein(s)
which are variant(s) of protein Sarcoplasmic reticulum
histidine-rich calcium-binding protein precursor (SEQ ID NO:389). A
description of each variant protein according to the present
invention is now provided.
Variant protein H88495_PEA.sub.--3_P15 (SEQ ID NO:309) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32) and H88495_PEA.sub.--3_T7 (SEQ ID NO:35). An alignment is
given to the known protein (Sarcoplasmic reticulum histidine-rich
calcium-binding protein precursor (SEQ ID NO:389)) at the end of
the application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between H88495_PEA.sub.--3_P15 (SEQ ID NO:309)
and SRCH_HUMAN_V1 (SEQ ID NO:346):
1. An isolated chimeric polypeptide encoding for
H88495_PEA.sub.--3_P 15 (SEQ ID NO:309), comprising a first amino
acid sequence being at least 90% homologous to
MGHHRPWLHASVLWAGVASLLLPPAMTQQLRGDGLGFRNRNN corresponding to amino
acids 1-42 of SRCH_HUMAN_V1 (SEQ ID NO:346), which also corresponds
to amino acids 1-42 of H88495_PEA.sub.--3.sub.13 P 15 (SEQ ID
NO:309), a bridging amino acid N corresponding to amino acid 43 of
H88495_PEA.sub.--3_P15 (SEQ ID NO:309), a second amino acid
sequence being at least 90% homologous to
TGVAGLSEEASAELRHHLHSPRDHPDENKDVSTENGHHFWSHPDREKEDEDVAKEYG
HLLPGHRSQDHKVGDEGVSGEEVFAEHGGQARGHRGHGSEDTEDSAEHRHHLPSHRS
HSHQDEDEDEVVSSEHHHHILRHGHRGHDGEDDEGEEEEEEEEEEEEASTEYGHQAHR
HRGHGSEEDEDVSDGHHHHGPSHRHQGHEEDDDDDDDDDDDDDDDDVSIEYRHQAH
RHQGHGIEEDEDVSDGHHHRDPSHRHRSHEEDDNDDDDVSTEYGHQAHRHQDHRKEE
VEAVSGEHHHHVPDHRHQGHRDEEEDEDVSTERWHQGPQHVHHGLVDEEEEEEEITV
QFGHYVASHQPRGHKSDEEDFQDEYKTEVPHHHHHRVPREEDEEVSAELGHQAPSHR
QSHQDEETGHGQRGSIKEMSHHPPGHTVVKDRSHLRKDDSEEEKEKEEDPGSHEEDDE
SSEQGEKGTHHGSRDQEDEEDEEEGHGLSLNQEEEEEEDKEEEEEEEDEERREERAEVG
APLSPDHSEEEEEEEEGLEEDEPRFTIIPNPLDRREEAGGASSEEESGEDTGPQDAQEYGN
YQPGSLCGYCSFCNRCTECESCHCDEENMGEHCDQCQ corresponding to amino acids
44-657 of SRCH_HUMAN_V1 (SEQ ID NO:346), which also corresponds to
amino acids 44-657 of H88495_PEA.sub.--3_P15 (SEQ ID NO:309), and a
third amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence VRPHLTLKAPLGLRMHRDPLRTPSPKSWPLTQPLTPDATLTPQAILTPTLT (SEQ
ID NO:418) corresponding to amino acids 658-708 of
H88495_PEA.sub.--3_P15 (SEQ ID NO:309), wherein said first amino
acid sequence, bridging amino acid, second amino acid sequence and
third amino acid sequence are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
H88495_PEA.sub.--3_P15 (SEQ ID NO:309), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VRPHLTLKAPLGLRMHRDPLRTPSPKSWPLTQPLTPDATLTPQAILTPTLT (SEQ ID NO:418)
in H88495_PEA.sub.--3_P 15 (SEQ ID NO:309).
It should be noted that the known protein sequence (SRCH_HUMAN; SEQ
ID NO:389) has one or more changes than the sequence given at the
end of the application and named as being the amino acid sequence
for SRCH_HUMAN_V1 (SEQ ID NO:346). These changes were previously
known to occur and are listed in the table below.
TABLE-US-00237 TABLE 5 Changes to SRCH_HUMAN_V1 (SEQ ID NO: 346)
SNP position(s) on amino acid sequence Type of change 97
Variant
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted. The protein localization is believed to be
secreted because both signal-peptide prediction programs predict
that this protein has a signal peptide, and neither trans-membrane
region prediction program predicts that this protein has a
trans-membrane region.
Variant protein H88495_PEA.sub.--3_P15 (SEQ ID NO:309) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 6, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein H88495_PEA.sub.--3_P15 (SEQ ID
NO:309) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00238 TABLE 6 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
6 P -> L No 6 P -> S No 43 N -> S Yes 96 A -> S Yes 364
Q -> No 580 D -> H Yes
Variant protein H88495_PEA.sub.--3_P15 (SEQ ID NO:309) is encoded
by the following transcript(s): H88495_PEA.sub.--3_T3 (SEQ ID
NO:31), H88495_PEA.sub.--3_T4 (SEQ ID NO:32) and
H88495_PEA.sub.--3_T7 (SEQ ID NO:35), for which the sequence(s)
is/are given at the end of the application.
The coding portion of transcript H88495_PEA.sub.--3_T3 (SEQ ID
NO:31) is shown in bold; this coding portion starts at position 743
and ends at position 2866. The transcript also has the following
SNPs as listed in Table 7 (given according to their position on the
nucleotide sequence, with the alternative nucleic acid listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein H88495_PEA.sub.--3P15 (SEQ ID
NO:309) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00239 TABLE 7 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> G Yes 285 C -> T Yes 362 A -> C Yes 373 G -> C
Yes 628 A -> T No 629 G -> T No 758 C -> T No 759 C ->
T No 847 G -> A Yes 870 A -> G Yes 958 G -> A No 1028 G
-> T Yes 1321 A -> G Yes 1834 G -> No 1903 C -> T Yes
2480 G -> C Yes
The coding portion of transcript H88495_PEA.sub.--3_T4 (SEQ ID
NO:32) is shown in bold; this coding portion starts at position 743
and ends at position 2866. The transcript also has the following
SNPs as listed in Table 8 (given according to their position on the
nucleotide sequence, with the alternative nucleic acid listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein H88495_PEA.sub.--3_P15 (SEQ ID
NO:309) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00240 TABLE 8 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> G Yes 285 C -> T Yes 362 A -> C Yes 373 G -> C
Yes 628 A -> T No 629 G -> T No 758 C -> T No 759 C ->
T No 847 G -> A Yes 870 A -> G Yes 958 G -> A No 1028 G
-> T Yes 1321 A -> G Yes 1834 G -> No 1903 C -> T Yes
2480 G -> C Yes 3225 G -> A Yes
The coding portion of transcript H88495_PEA.sub.13 3_T7 (SEQ ID
NO:35) is shown in bold; this coding portion starts at position 743
and ends at position 2866. The transcript also has the following
SNPs as listed in Table 9 (given according to their position on the
nucleotide sequence, with the alternative nucleic acid listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein H88495_PEA.sub.--3_P15 (SEQ ID
NO:309) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00241 TABLE 9 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> G Yes 285 C -> T Yes 362 A -> C Yes 373 G -> C
Yes 628 A -> T No 629 G -> T No 758 C -> T No 759 C ->
T No 847 G -> A Yes 870 A -> G Yes 958 G -> A No 1028 G
-> T Yes 1321 A -> G Yes 1834 G -> No 1903 C -> T Yes
2480 G -> C Yes 3106 T -> A Yes
Variant protein H88495_PEA.sub.--3_P16 (SEQ ID NO:310) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
H88495_PEA.sub.--3_T5 (SEQ ID NO:33) and H88495_PEA.sub.--3_T6 (SEQ
ID NO:34). An alignment is given to the known protein (Sarcoplasmic
reticulum histidine-rich calcium-binding protein precursor (SEQ ID
NO:389)) at the end of the application. One or more alignments to
one or more previously published protein sequences are given at the
end of the application. A brief description of the relationship of
the variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between H88495_PEA.sub.--3_P16 (SEQ ID NO:310)
and SRCH_HUMAN_V1 (SEQ ID NO:346):
1. An isolated chimeric polypeptide encoding for
H88495_PEA.sub.--3_P16 (SEQ ID NO:310), comprising a first amino
acid sequence being at least 90% homologous to
MGHHRPWLHASVLWAGVASLLLPPAMTQQLRGDGLGFRNRNN corresponding to amino
acids 1-42 of SRCH_HUMAN_V1 (SEQ ID NO:346), which also corresponds
to amino acids 1-42 of H88495_PEA.sub.--3_P 16 (SEQ ID NO:310), a
bridging amino acid N corresponding to amino acid 43 of
H88495_PEA.sub.--3_P16 (SEQ ID NO:310), a second amino acid
sequence being at least 90% homologous to
TGVAGLSEEASAELRHHLHSPRDHPDENKDVSTENGHHFWSHPDREKEDEDVAKEYG
HLLPGHRSQDHKVGDEGVSGEEVFAEHGGQARGHRGHGSEDTEDSAEHRHHLPSHRS
HSHQDEDEDEVVSSEHHHHILRHGHRGHDGEDDEGEEEEEEEEEEEEASTEYGHQAHR
HRGHGSEEDEDVSDGHHHHGPSHRHQGHEEDDDDDDDDDDDDDDDDVSIEYRHQAH
RHQGHGIEEDEDVSDGHHHRDPSHRHRSHEEDDNDDDDVSTEYGHQAHRHQDHRKEE
VEAVSGEHHHHVPDHRHQGHRDEEEDEDVSTERWHQGPQHVHHGLVDEEEEEEEITV
QFGHYVASHQPRGHKSDEEDFQDEYKTEVPHHHHHRVPREEDEEVSAELGHQAPSHR
QSHQDEETGHGQRGSIKEMSHHPPGHTVVKDRSHLRKDDSEEEKEKEEDPGSHEEDDE
SSEQGEKGTHHGSRDQEDEEDEEEGHGLSLNQEEEEEEDKEEEEEEEDEERREERAEVG
APLSPDHSEEEEEEEEGLEEDEPRFTIIPNPLDRREEAGGASSEEESGEDTGPQDAQEYGN
YQPGSLCGYCSFCNRCTECESCHCDEENMGEHCDQCQHCQFCYLCPLVCETVCAPG
corresponding to amino acids 44-676 of SRCH_HUMAN_V1 (SEQ ID
NO:346), which also corresponds to amino acids 44-676 of
H88495_PEA.sub.--3_P16 (SEQ ID NO:310), and a third amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence EHGRGPGKT
(SEQ ID NO:419) corresponding to amino acids 677-685 of
H88495_PEA.sub.--3_P16 (SEQ ID NO:310), wherein said first amino
acid sequence, bridging amino acid, second amino acid sequence and
third amino acid sequence are contiguous and in a sequential
order.
2. An isolated polypeptide encoding for a tail of
H88495_PEA.sub.--3_P16 (SEQ ID NO:310), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence EHGRGPGKT
(SEQ ID NO:419) in H88495_PEA.sub.--3_P16 (SEQ ID NO:310).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: membrane. The protein localization is believed to be
membrane because although it is a partial protein, because both
trans-membrane region prediction programs predict that this protein
has a trans-membrane region.
Variant protein H88495_PEA.sub.--3_P16 (SEQ ID NO:310) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 11, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein H88495_PEA.sub.--3_P16 (SEQ ID
NO:310) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00242 TABLE 11 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
6 P -> L No 6 P -> S No 43 N -> S Yes 96 A -> S Yes 364
Q -> No 580 D -> H Yes
Variant protein H88495_PEA.sub.--3_P16 (SEQ ID NO:310) is encoded
by the following transcript(s): H88495_PEA.sub.--3_T5 (SEQ ID
NO:33) and H88495_PEA.sub.--3_T6 (SEQ ID NO:34), for which the
sequence(s) is/are given at the end of the application.
The coding portion of transcript H88495_PEA.sub.--3_T5 (SEQ ID
NO:33) is shown in bold; this coding portion starts at position 743
and ends at position 2797. The transcript also has the following
SNPs as listed in Table 12 (given according to their position on
the nucleotide sequence, with the alternative nucleic acid listed;
the last column indicates whether the SNP is known or not; the
presence of known SNPs in variant protein H88495_PEA.sub.--3_P16
(SEQ ID NO:310) sequence provides support for the deduced sequence
of this variant protein according to the present invention).
TABLE-US-00243 TABLE 12 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> G Yes 285 C -> T Yes 362 A -> C Yes 373 G -> C
Yes 628 A -> T No 629 G -> T No 758 C -> T No 759 C ->
T No 847 G -> A Yes 870 A -> G Yes 958 G -> A No 1028 G
-> T Yes 1321 A -> G Yes 1834 G -> No 1903 C -> T Yes
2480 G -> C Yes 2855 T -> A Yes
The coding portion of transcript H88495_PEA.sub.--3_T6 (SEQ ID
NO:34) is shown in bold; this coding portion starts at position 743
and ends at position 2797. The transcript also has the following
SNPs as listed in Table 13 (given according to their position on
the nucleotide sequence, with the alternative nucleic acid listed;
the last column indicates whether the SNP is known or not; the
presence of known SNPs in variant protein H88495_PEA.sub.--3_P16
(SEQ ID NO:310) sequence provides support for the deduced sequence
of this variant protein according to the present invention).
TABLE-US-00244 TABLE 13 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> G Yes 285 C -> T Yes 362 A -> C Yes 373 G -> C
Yes 628 A -> T No 629 G -> T No 758 C -> T No 759 C ->
T No 847 G -> A Yes 870 A -> G Yes 958 G -> A No 1028 G
-> T Yes 1321 A -> G Yes 1834 G -> No 1903 C -> T Yes
2480 G -> C Yes 2855 T -> A Yes 3293 G -> A Yes
Variant protein H88495_PEA.sub.--3_P17 (SEQ ID NO:311) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
H88495_PEA.sub.--3_T8 (SEQ ID NO:36). An alignment is given to the
known protein (Sarcoplasmic reticulum histidine-rich
calcium-binding protein precursor (SEQ ID NO:389)) at the end of
the application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between H88495_PEA.sub.--3_P17 (SEQ ID NO:311)
and SRCH_HUMAN_V1 (SEQ ID NO:346):
1. An isolated chimeric polypeptide encoding for
H88495_PEA.sub.--3_P17 (SEQ ID NO:311), comprising a first amino
acid sequence being at least 90% homologous to
MCHHRPWLHASVLWAGVASLLLPPAMTQQLRGDGLGFRNRNN corresponding to amino
acids 1-42 of SRCH_HUMAN_V1 (SEQ ID NO:346), which also corresponds
to amino acids 1-42 of H88495_PEA.sub.--3_P17 (SEQ ID NO:311), a
bridging amino acid N corresponding to amino acid 43 of
H88495_PEA.sub.--3_P17 (SEQ ID NO:311), a second amino acid
sequence being at least 90% homologous to
TGVAGLSEEASAELRHHLHSPRDHPDENKDVSTENGHHFWSHPDREKEDEDVAKEYG
HLLPGHRSQDHKVGDEGVSGEEVFAEHGGQARGHRGHGSEDTEDSAEHRHHLPSHRS
HSHQDEDEDEVVSSEHHHHILRHGHRGHDGEDDEGEEEEEEEEEEEEASTEYGHQAHR
HRGHGSEEDEDVSDGHHHHGPSHRHQGHEEDDDDDDDDDDDDDDDDVSIEYRHQAH
RHQGHGIEEDEDVSDGHHHRDPSHRHRSHEEDDNDDDDVSTEYGHQAHRHQDHRKEE
VEAVSGEHHHHVPDHRHQGHRDEEEDEDVSTERWHQGPQHVHHGLVDEEEEEEEITV
QFGHYVASHQPRGHKSDEEDFQDEYKTEVPHHHHHRVPREEDEEVSAELGHQAPSHR
QSHQDEETGHGQRGSIKEMSHHPPGHTVVKDRSHLRKDDSEEEKEKEEDPGSHEEDDE
SSEQGEKGTHHGSRDQEDEEDEEEGHGLSLNQEEEEEEDKEEEEEEEDEERREERAEVG
APLSPDHSEEEEEEEEGLEEDEPRFTIIPNPLDRREEAGGASSEEESGEDTGPQDAQEYGN
YQPGSLCGYCSFCNRCTECESCHCDEENMGEHCDQCQ corresponding to amino acids
44-657 of SRCH_HUMAN_V1 (SEQ ID NO:346), which also corresponds to
amino acids 44-657 of H88495_PEA.sub.--3_P17 (SEQ ID NO:311), and a
third amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence GPGRHAGNAGTLTQSLDCDAGVPPPAFQPLSTSYIYFSE (SEQ ID NO:420)
corresponding to amino acids 658-696 of H88495_PEA.sub.--3_P17 (SEQ
ID NO:311), wherein said first amino acid sequence, bridging amino
acid, second amino acid sequence and third amino acid sequence are
contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
H88495_PEA.sub.--3_P17 (SEQ ID NO:311), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
GPGRHAGNAGTLTQSLDCDAGVPPPAFQPLSTSYIYFSE (SEQ ID NO:420) in
H88495_PEA.sub.--3_P17 (SEQ ID NO:311).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted. The protein localization is believed to be
secreted because both signal-peptide prediction programs predict
that this protein has a signal peptide, and neither trans-membrane
region prediction program predicts that this protein has a
trans-membrane region.
Variant protein H88495_PEA.sub.--3_P17 (SEQ ID NO:311) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 15, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein H88495_PEA.sub.--3_P17 (SEQ ID
NO:311) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00245 TABLE 15 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
6 P -> L No 6 P -> S No 43 N -> S Yes 96 A -> S Yes 364
Q -> No 580 D -> H Yes
Variant protein H88495_PEA.sub.--3_P17 (SEQ ID NO:311) is encoded
by the following transcript(s): H88495_PEA.sub.--3_T8 (SEQ ID
NO:36), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript H88495_PEA.sub.--3_T8
(SEQ ID NO:36) is shown in bold; this coding portion starts at
position 743 and ends at position 2830. The transcript also has the
following SNPs as listed in Table 16 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
H88495_PEA.sub.--3_P17 (SEQ ID NO:311) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00246 TABLE 16 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> G Yes 285 C -> T Yes 362 A -> C Yes 373 G -> C
Yes 628 A -> T No 629 G -> T No 758 C -> T No 759 C ->
T No 847 G -> A Yes 870 A -> G Yes 958 G -> A No 1028 G
-> T Yes 1321 A -> G Yes 1834 G -> No 1903 C -> T Yes
2480 G -> C Yes 2882 G -> A Yes
Variant protein H88495_PEA.sub.--3_P18 (SEQ ID NO:312) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
H88495_PEA.sub.--3_T9 (SEQ ID NO:37). An alignment is given to the
known protein (Sarcoplasmic reticulum histidine-rich
calcium-binding protein precursor (SEQ ID NO:389)) at the end of
the application. One or more alignments to one or more previously
published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between H88495_PEA.sub.--3_P18 (SEQ ID NO:312)
and SRCH_HUMAN_V1 (SEQ ID NO:346):
1. An isolated chimeric polypeptide encoding for
H88495_PEA.sub.--3_P18 (SEQ ID NO:312), comprising a first amino
acid sequence being at least 90% homologous to
MGHHRPWLHASVLWAGVASLLLPPAMTQQLRGDGLGFRNRNN corresponding to amino
acids 1-42 of SRCH_HUMAN_V1 (SEQ ID NO:346), which also corresponds
to amino acids 1-42 of H88495_PEA.sub.--3_P18 (SEQ ID NO:312), a
bridging amino acid N corresponding to amino acid 43 of
H88495_PEA.sub.--3_P18 (SEQ ID NO:312), a second amino acid
sequence being at least 90% homologous to
TGVAGLSEEASAELRHHLHSPRDHPDENKDVSTENGHHFWSHPDREKEDEDVAKEYG
HLLPGHRSQDHKVGDEGVSGEEVFAEHGGQARGHRGHGSEDTEDSAEHRHHLPSHRS
HSHQDEDEDEVVSSEHHHHILRHGHRGHDGEDDEGEEEEEEEEEEEEASTEYGHQAHR
HRGHGSEEDEDVSDGHHHHGPSHRHQGHEEDDDDDDDDDDDDDDDDVSIEYRHQAH
RHQGHGIEEDEDVSDGHHHRDPSHRHRSHEEDDNDDDDVSTEYGHQAHRHQDHRKEE
VEAVSGEHHHHVPDHRHQGHRDEEEDEDVSTERWHQGPQHVHHGLVDEEEEEEEITV
QFGHYVASHQPRGHKSDEEDFQDEYKTEVPHHHHHRVPREEDEEVSAELGHQAPSHR
QSHQDEETGHGQRGSIKEMSHHPPGHTVVKDRSHLRKDDSEEEKEKEEDPGSHEEDDE
SSEQGEKGTHHGSRDQEDEEDEEEGHGLSLNQEEEEEEDKEEEEEEEDEERREERAEVG
APLSPDHSEEEEEEEEGLEEDEPRFTIIPNPLDRREEAGGASSEEESGEDT corresponding
to amino acids 44-610 of SRCH_HUMAN_V1 (SEQ ID NO:346), which also
corresponds to amino acids 44-610 of H88495_PEA.sub.--3_P18 (SEQ ID
NO:312), and a third amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence AMH corresponding to amino acids
611-613 of H88495_PEA.sub.--3_P18 (SEQ ID NO:312), wherein said
first amino acid sequence, bridging amino acid, second amino acid
sequence and third amino acid sequence are contiguous and in a
sequential order.
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: secreted. The protein localization is believed to be
secreted because both signal-peptide prediction programs predict
that this protein has a signal peptide, and neither trans-membrane
region prediction program predicts that this protein has a
trans-membrane region.
Variant protein H88495_PEA.sub.--3_P18 (SEQ ID NO:312) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 18, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein H88495_PEA.sub.--3_P18 (SEQ ID
NO:312) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00247 TABLE 18 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
6 P -> L No 6 P -> S No 43 N -> S Yes 96 A -> S Yes 364
Q -> No 580 D -> H Yes
Variant protein H88495_PEA.sub.--3_P18 (SEQ ID NO:312) is encoded
by the following transcript(s): H88495_PEA.sub.--3_T9 (SEQ ID
NO:37), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript H88495_PEA.sub.--3_T9
(SEQ ID NO:37) is shown in bold; this coding portion starts at
position 743 and ends at position 2581. The transcript also has the
following SNPs as listed in Table 19 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
H88495_PEA.sub.--3_P18 (SEQ ID NO:312) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00248 TABLE 19 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
223 A -> G Yes 285 C -> T Yes 362 A -> C Yes 373 G -> C
Yes 628 A -> T No 629 G -> T No 758 C -> T No 759 C ->
T No 847 G -> A Yes 870 A -> G Yes 958 G -> A No 1028 G
-> T Yes 1321 A -> G Yes 1834 G -> No 1903 C -> T Yes
2480 G -> C Yes
As noted above, cluster H88495 features 22 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster H88495_PEA.sub.--3_node.sub.--0 (SEQ ID NO:164)
according to the present invention is supported by 12 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 20 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00249 TABLE 20 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 1 665 H88495_PEA_3_T4 (SEQ ID NO:
32) 1 665 H88495_PEA_3_T5 (SEQ ID NO: 33) 1 665 H88495_PEA_3_T6
(SEQ ID NO: 34) 1 665 H88495_PEA_3_T7 (SEQ ID NO: 35) 1 665
H88495_PEA_3_T8 (SEQ ID NO: 36) 1 665 H88495_PEA_3_T9 (SEQ ID NO:
37) 1 665
Segment cluster H88495_PEA.sub.--3_node.sub.--1 (SEQ ID NO:165)
according to the present invention is supported by 18 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 21 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00250 TABLE 21 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 666 1178 H88495_PEA_3_T4 (SEQ ID
NO: 32) 666 1178 H88495_PEA_3_T5 (SEQ ID NO: 33) 666 1178
H88495_PEA_3_T6 (SEQ ID NO: 34) 666 1178 H88495_PEA_3_T7 (SEQ ID
NO: 35) 666 1178 H88495_PEA_3_T8 (SEQ ID NO: 36) 666 1178
H88495_PEA_3_T9 (SEQ ID NO: 37) 666 1178
Segment cluster H88495_PEA.sub.--3_node.sub.--4 (SEQ ID NO:166)
according to the present invention is supported by 22 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 22 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00251 TABLE 22 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 1210 1646 H88495_PEA_3_T4 (SEQ ID
NO: 32) 1210 1646 H88495_PEA_3_T5 (SEQ ID NO: 33) 1210 1646
H88495_PEA_3_T6 (SEQ ID NO: 34) 1210 1646 H88495_PEA_3_T7 (SEQ ID
NO: 35) 1210 1646 H88495_PEA_3_T8 (SEQ ID NO: 36) 1210 1646
H88495_PEA_3_T9 (SEQ ID NO: 37) 1210 1646
Segment cluster H88495_PEA.sub.--3_node.sub.--9 (SEQ ID NO:167)
according to the present invention is supported by 31 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 23 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00252 TABLE 23 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 1819 2335 H88495_PEA_3_T4 (SEQ ID
NO: 32) 1819 2335 H88495_PEA_3_T5 (SEQ ID NO: 33) 1819 2335
H88495_PEA_3_T6 (SEQ ID NO: 34) 1819 2335 H88495_PEA_3_T7 (SEQ ID
NO: 35) 1819 2335 H88495_PEA_3_T8 (SEQ ID NO: 36) 1819 2335
H88495_PEA_3_T9 (SEQ ID NO: 37) 1819 2335
Segment cluster H88495_PEA.sub.--3_node.sub.--13 (SEQ ID NO:168)
according to the present invention is supported by 34 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 24 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00253 TABLE 24 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 2378 2509 H88495_PEA_3_T4 (SEQ ID
NO: 32) 2378 2509 H88495_PEA_3_T5 (SEQ ID NO: 33) 2378 2509
H88495_PEA_3_T6 (SEQ ID NO: 34) 2378 2509 H88495_PEA_3_T7 (SEQ ID
NO: 35) 2378 2509 H88495_PEA_3_T8 (SEQ ID NO: 36) 2378 2509
H88495_PEA_3_T9 (SEQ ID NO: 37) 2378 2509
Segment cluster H88495_PEA.sub.--3_node.sub.--19 (SEQ ID NO:169)
according to the present invention is supported by 4 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32) and H88495_PEA.sub.--3_T7 (SEQ ID NO:35). Table 25 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00254 TABLE 25 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 2714 2964 H88495_PEA_3_T4 (SEQ ID
NO: 32) 2714 2964 H88495_PEA_3_T7 (SEQ ID NO: 35) 2714 2964
Segment cluster H88495_PEA.sub.--3_node.sub.--21 (SEQ ID NO:170)
according to the present invention is supported by 1 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6 (SEQ ID
NO:34) and H88495_PEA.sub.--3_T7 (SEQ ID NO:35). Table 26 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00255 TABLE 26 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T5 (SEQ ID NO: 33) 2769 3095 H88495_PEA_3_T6 (SEQ ID
NO: 34) 2769 3095 H88495_PEA_3_T7 (SEQ ID NO: 35) 3020 3346
Segment cluster H88495_PEA.sub.--3_node.sub.--26 (SEQ ID NO:171)
according to the present invention is supported by 26 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 27 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00256 TABLE 27 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 3057 3189 H88495_PEA_3_T4 (SEQ ID
NO: 32) 3057 3298 H88495_PEA_3_T5 (SEQ ID NO: 33) 3125 3257
H88495_PEA_3_T6 (SEQ ID NO: 34) 3125 3366 H88495_PEA_3_T7 (SEQ ID
NO: 35) 3376 3508 H88495_PEA_3_T8 (SEQ ID NO: 36) 2714 2955
H88495_PEA_3_T9 (SEQ ID NO: 37) 2735 2867
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster H88495_PEA.sub.--3_node.sub.--2 (SEQ ID NO:172)
according to the present invention is supported by 14 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 28 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00257 TABLE 28 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 1179 1209 H88495_PEA_3_T4 (SEQ ID
NO: 32) 1179 1209 H88495_PEA_3_T5 (SEQ ID NO: 33) 1179 1209
H88495_PEA_3_T6 (SEQ ID NO: 34) 1179 1209 H88495_PEA_3_T7 (SEQ ID
NO: 35) 1179 1209 H88495_PEA_3_T8 (SEQ ID NO: 36) 1179 1209
H88495_PEA_3_T9 (SEQ ID NO: 37) 1179 1209
Segment cluster H88495_PEA.sub.--3_node.sub.--5 (SEQ ID NO:173)
according to the present invention is supported by 16 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 29 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00258 TABLE 29 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 1647 1676 H88495_PEA_3_T4 (SEQ ID
NO: 32) 1647 1676 H88495_PEA_3_T5 (SEQ ID NO: 33) 1647 1676
H88495_PEA_3_T6 (SEQ ID NO: 34) 1647 1676 H88495_PEA_3_T7 (SEQ ID
NO: 35) 1647 1676 H88495_PEA_3_T8 (SEQ ID NO: 36) 1647 1676
H88495_PEA_3_T9 (SEQ ID NO: 37) 1647 1676
Segment cluster H88495_PEA.sub.--3_node.sub.--6 (SEQ ID NO:174)
according to the present invention is supported by 14 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 30 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00259 TABLE 30 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 1677 1763 H88495_PEA_3_T4 (SEQ ID
NO: 32) 1677 1763 H88495_PEA_3_T5 (SEQ ID NO: 33) 1677 1763
H88495_PEA_3_T6 (SEQ ID NO: 34) 1677 1763 H88495_PEA_3_T7 (SEQ ID
NO: 35) 1677 1763 H88495_PEA_3_T8 (SEQ ID NO: 36) 1677 1763
H88495_PEA_3_T9 (SEQ ID NO: 37) 1677 1763
Segment cluster H88495_PEA.sub.--3_node.sub.--7 (SEQ ID NO:175)
according to the present invention can be found in the following
transcript(s): H88495_PEA.sub.--3_T3 (SEQ ID NO:31),
H88495_PEA.sub.--3_T4 (SEQ ID NO:32), H88495_PEA.sub.--3_T5 (SEQ ID
NO:33), H88495_PEA.sub.--3_T6 (SEQ ID NO:34), H88495_PEA.sub.--3_T7
(SEQ ID NO:35), H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and
H88495_PEA.sub.--3_T9 (SEQ ID NO:37). Table 31 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00260 TABLE 31 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 1764 1773 H88495_PEA_3_T4 (SEQ ID
NO: 32) 1764 1773 H88495_PEA_3_T5 (SEQ ID NO: 33) 1764 1773
H88495_PEA_3_T6 (SEQ ID NO: 34) 1764 1773 H88495_PEA_3_T7 (SEQ ID
NO: 35) 1764 1773 H88495_PEA_3_T8 (SEQ ID NO: 36) 1764 1773
H88495_PEA_3_T9 (SEQ ID NO: 37) 1764 1773
Segment cluster H88495_PEA.sub.--3_node.sub.--8 (SEQ ID NO:176)
according to the present invention is supported by 19 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 32 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00261 TABLE 32 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 1774 1818 H88495_PEA_3_T4 (SEQ ID
NO: 32) 1774 1818 H88495_PEA_3_T5 (SEQ ID NO: 33) 1774 1818
H88495_PEA_3_T6 (SEQ ID NO: 34) 1774 1818 H88495_PEA_3_T7 (SEQ ID
NO: 35) 1774 1818 H88495_PEA_3_T8 (SEQ ID NO: 36) 1774 1818
H88495_PEA_3_T9 (SEQ ID NO: 37) 1774 1818
Segment cluster H88495_PEA.sub.--3_node.sub.--10 (SEQ ID NO:177)
according to the present invention can be found in the following
transcript(s): H88495_PEA.sub.--3_T3 (SEQ ID NO:31),
H88495_PEA.sub.--3_T4 (SEQ ID NO:32), H88495_PEA.sub.--3_T5 (SEQ ID
NO:33), H88495_PEA.sub.--3_T6 (SEQ ID NO:34), H88495_PEA.sub.--3_T7
(SEQ ID NO:35), H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and
H88495_PEA.sub.--3_T9 (SEQ ID NO:37). Table 33 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00262 TABLE 33 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 2336 2353 H88495_PEA_3_T4 (SEQ ID
NO: 32) 2336 2353 H88495_PEA_3_T5 (SEQ ID NO: 33) 2336 2353
H88495_PEA_3_T6 (SEQ ID NO: 34) 2336 2353 H88495_PEA_3_T7 (SEQ ID
NO: 35) 2336 2353 H88495_PEA_3_T8 (SEQ ID NO: 36) 2336 2353
H88495_PEA_3_T9 (SEQ ID NO: 37) 2336 2353
Segment cluster H88495_PEA.sub.--3_node.sub.--11 (SEQ ID NO:178)
according to the present invention can be found in the following
transcript(s): H88495_PEA.sub.--3_T3 (SEQ ID NO:31),
H88495_PEA.sub.--3_T4 (SEQ ID NO:32), H88495_PEA.sub.--3_T5 (SEQ ID
NO:33), H88495_PEA.sub.--3_T6 (SEQ ID NO:34), H88495_PEA.sub.--3_T7
(SEQ ID NO:35), H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and
H88495_PEA.sub.--3_T9 (SEQ ID NO:37). Table 34 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00263 TABLE 34 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 2354 2362 H88495_PEA_3_T4 (SEQ ID
NO: 32) 2354 2362 H88495_PEA_3_T5 (SEQ ID NO: 33) 2354 2362
H88495_PEA_3_T6 (SEQ ID NO: 34) 2354 2362 H88495_PEA_3_T7 (SEQ ID
NO: 35) 2354 2362 H88495_PEA_3_T8 (SEQ ID NO: 36) 2354 2362
H88495_PEA_3_T9 (SEQ ID NO: 37) 2354 2362
Segment cluster H88495_PEA.sub.--3_node.sub.--12 (SEQ ID NO:179)
according to the present invention can be found in the following
transcript(s): H88495_PEA.sub.--3_T3 (SEQ ID NO:31),
H88495_PEA.sub.--3_T4 (SEQ ID NO:32), H88495_PEA.sub.--3_T5 (SEQ ID
NO:33), H88495_PEA 3_T6 (SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ
ID NO:35), H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and
H88495_PEA.sub.--3_T9 (SEQ ID NO:37). Table 35 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00264 TABLE 35 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 2363 2377 H88495_PEA_3_T4 (SEQ ID
NO: 32) 2363 2377 H88495_PEA_3_T5 (SEQ ID NO: 33) 2363 2377
H88495_PEA_3_T6 (SEQ ID NO: 34) 2363 2377 H88495_PEA_3_T7 (SEQ ID
NO: 35) 2363 2377 H88495_PEA_3_T8 (SEQ ID NO: 36) 2363 2377
H88495_PEA_3_T9 (SEQ ID NO: 37) 2363 2377
Segment cluster H88495_PEA.sub.--3_node.sub.--14 (SEQ ID NO:180)
according to the present invention is supported by 33 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 36 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00265 TABLE 36 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 2510 2573 H88495_PEA_3_T4 (SEQ ID
NO: 32) 2510 2573 H88495_PEA_3_T5 (SEQ ID NO: 33) 2510 2573
H88495_PEA_3_T6 (SEQ ID NO: 34) 2510 2573 H88495_PEA_3_T7 (SEQ ID
NO: 35) 2510 2573 H88495_PEA_3_T8 (SEQ ID NO: 36) 2510 2573
H88495_PEA_3_T9 (SEQ ID NO: 37) 2510 2573
Segment cluster H88495_PEA.sub.--3_node.sub.--16 (SEQ ID NO:181)
according to the present invention is supported by 33 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35) and
H88495_PEA.sub.--3_T8 (SEQ ID NO:36). Table 37 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00266 TABLE 37 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 2574 2644 H88495_PEA_3_T4 (SEQ ID
NO: 32) 2574 2644 H88495_PEA_3_T5 (SEQ ID NO: 33) 2574 2644
H88495_PEA_3_T6 (SEQ ID NO: 34) 2574 2644 H88495_PEA_3_T7 (SEQ ID
NO: 35) 2574 2644 H88495_PEA_3_T8 (SEQ ID NO: 36) 2574 2644
Segment cluster H88495_PEA.sub.--3_node.sub.--18 (SEQ ID NO:182)
according to the present invention is supported by 31 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35),
H88495_PEA.sub.--3_T8 (SEQ ID NO:36) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 38 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00267 TABLE 38 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 2645 2713 H88495_PEA_3_T4 (SEQ ID
NO: 32) 2645 2713 H88495_PEA_3_T5 (SEQ ID NO: 33) 2645 2713
H88495_PEA_3_T6 (SEQ ID NO: 34) 2645 2713 H88495_PEA_3_T7 (SEQ ID
NO: 35) 2645 2713 H88495_PEA_3_T8 (SEQ ID NO: 36) 2645 2713
H88495_PEA_3_T9 (SEQ ID NO: 37) 2574 2642
Segment cluster H88495_PEA.sub.--3_node.sub.--20 (SEQ ID NO:183)
according to the present invention is supported by 27 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35) and
H88495_PEA.sub.--3_T9 (SEQ ID NO:37). Table 39 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00268 TABLE 39 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 2965 3019 H88495_PEA_3_T4 (SEQ ID
NO: 32) 2965 3019 H88495_PEA_3_T5 (SEQ ID NO: 33) 2714 2768
H88495_PEA_3_T6 (SEQ ID NO: 34) 2714 2768 H88495_PEA_3_T7 (SEQ ID
NO: 35) 2965 3019 H88495_PEA_3_T9 (SEQ ID NO: 37) 2643 2697
Segment cluster H88495_PEA.sub.--3_node.sub.--23 (SEQ ID NO:184)
according to the present invention can be found in the following
transcript(s): H88495_PEA.sub.--3_T3 (SEQ ID NO:31),
H88495_PEA.sub.--3_T4 (SEQ ID NO:32) and H88495_PEA.sub.--3_T9 (SEQ
ID NO:37). Table 40 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00269 TABLE 40 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 3020 3027 H88495_PEA_3_T4 (SEQ ID
NO: 32) 3020 3027 H88495_PEA_3_T9 (SEQ ID NO: 37) 2698 2705
Segment cluster H88495_PEA.sub.--3_node.sub.--24 (SEQ ID NO:185)
according to the present invention is supported by 23 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
H88495_PEA.sub.--3_T3 (SEQ ID NO:31), H88495_PEA.sub.--3_T4 (SEQ ID
NO:32), H88495_PEA.sub.--3_T5 (SEQ ID NO:33), H88495_PEA.sub.--3_T6
(SEQ ID NO:34), H88495_PEA.sub.--3_T7 (SEQ ID NO:35) and
H88495_PEA.sub.--3_T9 (SEQ ID NO:37). Table 41 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00270 TABLE 41 Segment location on transcripts Segment
Segment starting ending Transcript name position position
H88495_PEA_3_T3 (SEQ ID NO: 31) 3028 3056 H88495_PEA_3_T4 (SEQ ID
NO: 32) 3028 3056 H88495_PEA_3_T5 (SEQ ID NO: 33) 3096 3124
H88495_PEA_3_T6 (SEQ ID NO: 34) 3096 3124 H88495_PEA_3_T7 (SEQ ID
NO: 35) 3347 3375 H88495_PEA_3_T9 (SEQ ID NO: 37) 2706 2734
Variant Protein Alignment to the Previously Known Protein: Sequence
name: SRCH_HUMAN_V1 (SEQ ID NO:346) Sequence documentation:
Alignment of: H88495_PEA.sub.--3_P15 (SEQ ID NO:309)+SRCH_HUMAN_V1
(SEQ NO:346).
TABLE-US-00271 Alignment segment 1/1: Quality: 6726.00 Escore: 0
Matching length: 657 Total length: 657 Matching Percent Similarity:
100.00 Matching Percent 99.85 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 99.85 Gaps: 0
Alignment:
##STR00035## Sequence name: SRCH_HUMAN_V1 (SEQ ID NO:346) Sequence
documentation: Alignment of: H88495_PEA.sub.--3_P16 (SEQ ID
NO:310)+SRCH_HUMAN_V1 (SEQ ID NO:346).
TABLE-US-00272 Alignment segment 1/1: Quality: 6935.00 Escore: 0
Matching length: 676 Total length: 676 Matching Percent Similarity:
100.00 Matching Percent 99.85 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 99.85 Gaps: 0
Alignment:
##STR00036## Sequence name: SRCH_HUMAN_V1 (SEQ ID NO:346) Sequence
documentation: Alignment of: H88495_PEA.sub.--3_P17 (SEQ ID
NO:311)+SRCH_HUMAN_V1 (SEQ ID NO:346).
TABLE-US-00273 Alignment segment 1/1: Quality: 6726.00 Escore: 0
Matching length: 657 Total length: 657 Matching Percent Similarity:
100.00 Matching Percent 99.85 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 99.85 Gaps: 0
Alignment:
##STR00037## Sequence name: SRCH_HUMAN_V1 (SEQ ID NO:346) Sequence
documentation: Alignment of: H88495_PEA.sub.--3_P18 (SEQ ID
NO:312)+SRCH_HUMAN_V1 (SEQ ID NO:346).
TABLE-US-00274 Alignment segment 1/1: Quality: 6206.00 Escore: 0
Matching length: 610 Total length: 610 Matching Percent Similarity:
100.00 Matching Percent 99.84 Identity: Total Percent Similarity:
100.00 Total Percent Identity: 99.84 Gaps: 0
Alignment:
##STR00038##
Description for Cluster Z36249
Cluster Z36249 features 4 transcript(s) and 11 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00275 TABLE 1 Transcripts of interest Transcript Name Seq
ID No. Z36249_PEA_3_T2 38 Z36249_PEA_3_T3 39 Z36249_PEA_3_T5 40
Z36249_PEA_3_T9 41
TABLE-US-00276 TABLE 2 Segments of interest Segment Name Seq ID No.
Z36249_PEA_3_node_0 186 Z36249_PEA_3_node_3 187 Z36249_PEA_3_node_5
188 Z36249_PEA_3_node_11 189 Z36249_PEA_3_node_14 190
Z36249_PEA_3_node_24 191 Z36249_PEA_3_node_10 192
Z36249_PEA_3_node_13 193 Z36249_PEA_3_node_17 194
Z36249_PEA_3_node_19 195 Z36249_PEA_3_node_21 196
TABLE-US-00277 TABLE 3 Proteins of interest Seq Protein Name ID No.
Corresponding Transcript(s) Z36249_PEA_3_P2 313 Z36249_PEA_3_T2
(SEQ ID NO: 38) Z36249_PEA_3_P3 314 Z36249_PEA_3_T3 (SEQ ID NO: 39)
Z36249_PEA_3_P4 315 Z36249_PEA_3_T5 (SEQ ID NO: 40) Z36249_PEA_3_P5
316 Z36249_PEA_3_T9 (SEQ ID NO: 41)
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster Z36249. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 27 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 27, concerning the number of
heart-specific clones in libraries/sequences; as well as with
regard to the histogram in FIG. 28, concerning the actual
expression of oligonucleotides in various tissues, including
heart.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs, which was found to be 33.8; the ratio of
expression of the cluster in heart specific ESTs to the overall
expression of the cluster in muscle-specific ESTs which was found
to be 27.8; and fisher exact test P-values were computed both for
library and weighted clone counts to check that the counts are
statistically significant, and were found to be 1.60E-47.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the ratio of expression of the cluster
in heart specific ESTs to the overall expression of the cluster in
muscle-specific ESTs which was found to be 33.8, which clearly
supports specific expression in heart tissue
As noted above, cluster Z36249 features 4 transcript(s), which were
listed in Table 1 above. A description of each variant protein
according to the present invention is now provided.
Variant protein Z36249_PEA.sub.--3_P2 (SEQ ID NO:313) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z36249_PEA.sub.--3_T2 (SEQ ID NO:38). One or more alignments to one
or more previously published protein sequences are given at the end
of the application. A brief description of the relationship of the
variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between Z36249_PEA.sub.--3_P2 (SEQ ID NO:313) and
Q96LE7 (SEQ ID NO:344):
1. An isolated chimeric polypeptide encoding for
Z36249_PEA.sub.--3_P2 (SEQ ID NO:313), comprising a first amino
acid sequence being at least 90% homologous to
MMVLKVEELVTGKKNGNGEAGEFLPEDFRDGEYEAAVTLEKQEDLKTLLAHPVTLGE
QQWKSEKQREAELKKKKLEQRSKLENLEDLEIIIQLKKRKKYRKTKVPVVKEPEPEII
corresponding to amino acids 1-115 of Q96LE7 (SEQ ID NO:344), which
also corresponds to amino acids 1-115 of Z36249_PEA.sub.--3_P2 (SEQ
ID NO:313), and a second amino acid sequence being at least 90%
homologous to
YKRTALHRACLEGHLAIVEKLMEAGAQIEFRDMLESTAIHWASRGGNLDVLKLLLNKG
AKISARDKLLSTALHVAVRTGHYECAEHLIACEADLNAKDREGDTPLHDAVRLNRYK
MIRLLIMYGADLNIKNCAGKTPMDLVLHWQNGTKAIFDSLRENSYKTSRIATF corresponding
to amino acids 152-319 of Q96LE7 (SEQ ID NO:344), which also
corresponds to amino acids 116-283 of Z36249_PEA.sub.--3_P2 (SEQ ID
NO:313), wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
2. An isolated chimeric polypeptide encoding for an edge portion of
Z36249_PEA.sub.--3_P2 (SEQ ID NO:313), comprising a polypeptide
having a length "n", wherein n is at least about 10 amino acids in
length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably
at least about 40 amino acids in length and most preferably at
least about 50 amino acids in length, wherein at least two amino
acids comprise IY, having a structure as follows: a sequence
starting from any of amino acid numbers 115-x to 115; and ending at
any of amino acid numbers 116+((n-2)-x), in which x varies from 0
to n-2.
Comparison report between Z36249_PEA.sub.--3_P2 (SEQ ID NO:313) and
Q15327 (SEQ ID NO:345):
1. An isolated chimeric polypeptide encoding for
Z36249_PEA.sub.--3_P2 (SEQ ID NO:313), comprising a first amino
acid sequence being at least 90% homologous to
MMVLKVEELVTGKKNGNGEAGEFLPEDFRDGEYEAAVTLEKQEDLKTLLAHPVTLGE
QQWKSEKQREAEL corresponding to amino acids 1-70 of Q15327 (SEQ ID
NO:345), which also corresponds to amino acids 1-70 of
Z36249_PEA.sub.--3_P2 (SEQ ID NO:313), a bridging amino acid K
corresponding to amino acid 71 of Z36249_PEA.sub.--3_P2 (SEQ ID
NO:313), a second amino acid sequence being at least 90% homologous
to KKKLEQRSKLENLEDLEIIIQLKKRKKYRKTKVPVVKEPEPEII corresponding to
amino acids 72-115 of Q15327 (SEQ ID NO:345), which also
corresponds to amino acids 72-115 of Z36249_PEA.sub.--3_P2 (SEQ ID
NO:313), and a third amino acid sequence being at least 90%
homologous to
YKRTALHRACLEGHLAIVEKLMEAGAQIEFRDMLESTAIHWASRGGNLDVLKLLLNKG
AKISARDKLLSTALHVAVRTGHYECAEHLIACEADLNAKDREGDTPLHDAVRLNRYK
MIRLLIMYGADLNIKNCAGKTPMDLVLHWQNGTKAIFDSLRENSYKTSRIATF corresponding
to amino acids 152-319 of Q15327 (SEQ ID NO:345), which also
corresponds to amino acids 116-283 of Z36249_PEA.sub.--3_P2 (SEQ ID
NO:313), wherein said first amino acid sequence, bridging amino
acid, second amino acid sequence and third amino acid sequence are
contiguous and in a sequential order.
2. An isolated chimeric polypeptide encoding for an edge portion of
Z36249_PEA.sub.--3_P2 (SEQ ID NO:313), comprising a polypeptide
having a length "n", wherein n is at least about 10 amino acids in
length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably
at least about 40 amino acids in length and most preferably at
least about 50 amino acids in length, wherein at least two amino
acids comprise IY, having a structure as follows: a sequence
starting from any of amino acid numbers 115-x to 115; and ending at
any of amino acid numbers 116+((n-2)-x), in which x varies from 0
to n-2.
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein Z36249_PEA.sub.--3_P2 (SEQ ID NO:313) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 4, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein Z36249_PEA.sub.--3_P2 (SEQ ID
NO:313) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00278 TABLE 4 Amino acid mutations SNP position(s) on
amino acid Alternative sequence amino acid(s) Previously known SNP?
34 E -> * Yes
Variant protein Z36249_PEA.sub.--3_P2 (SEQ ID NO:313) is encoded by
the following transcript(s): Z36249_PEA.sub.--3_T2 (SEQ ID NO:38),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript Z36249_PEA.sub.--3_T2
(SEQ ID NO:38) is shown in bold; this coding portion starts at
position 250 and ends at position 1098. The transcript also has the
following SNPs as listed in Table 5 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
Z36249_PEA.sub.--3_P2 (SEQ ID NO:313) sequence provides support for
the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00279 TABLE 5 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
105 T -> C Yes 208 T -> No 349 G -> T Yes 459 C -> A No
1160 A -> G Yes 1356 C -> T Yes 1417 C -> T Yes 1516 C
-> T Yes 1601 C -> T Yes 1705 G -> A Yes 1761 G -> A
Yes 1969 G -> A Yes 1974 G -> A Yes 2047 G -> A Yes
Variant protein Z36249_PEA.sub.--3_P3 (SEQ ID NO:314) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z36249_PEA.sub.--3_T3 (SEQ ID NO:39). One or more alignments to one
or more previously published protein sequences are given at the end
of the application. A brief description of the relationship of the
variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between Z36249.sub.13 PEA.sub.--3_P3 (SEQ ID
NO:314) and Q96LE7 (SEQ ID NO:344):
1. An isolated chimeric polypeptide encoding for
Z36249_PEA.sub.--3_P3 (SEQ ID NO:314), comprising a first amino
acid sequence being at least 90% homologous to
MMVLKVEELVTGKKNGNGEAGEFLPEDFRDGEYEAAVTLEKQEDLKTLLAHPVTLGE
QQWKSEKQREAELKKKKLEQRSKLENLEDLEIIIQLKKRKKYRKTKVPVVKEPEPEIITE
PVDVPTFLKAALENKLPVVEKFLSDKNNPDVCDEYKRTALHRACLEGHLAIVEKLMEA
GAQIEFRDM corresponding to amino acids 1-184 of Q96LE7 (SEQ ID
NO:344), which also corresponds to amino acids 1-184 of
Z36249_PEA.sub.--3_P3 (SEQ ID NO:314), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
VNIFLCLGMSQKK (SEQ ID NO:421) corresponding to amino acids 185-197
of Z36249_PEA.sub.--3_P3 (SEQ ID NO:314), wherein said first amino
acid sequence and second amino acid sequence are contiguous and in
a sequential order.
2. An isolated polypeptide encoding for a tail of
Z36249_PEA.sub.--3_P3 (SEQ ID NO:314), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VNIFLCLGMSQKK (SEQ ID NO:421) in Z36249_PEA.sub.--3_P3 (SEQ ID
NO:314).
Comparison report between Z36249_PEA.sub.--3_P3 (SEQ ID NO:314) and
Q15327 (SEQ ID NO:345):
1. An isolated chimeric polypeptide encoding for
Z36249_PEA.sub.--3_P3 (SEQ ID NO:314), comprising a first amino
acid sequence being at least 90% homologous to
MMVLKVEELVTGKKNGNGEAGEFLPEDFRDGEYEAAVTLEKQEDLKTLLAHPVTLGE
QQWKSEKQREAEL corresponding to amino acids 1-70 of Q15327 (SEQ ID
NO:345), which also corresponds to amino acids 1-70 of
Z36249_PEA.sub.--3_P3 (SEQ ID NO:314), a bridging amino acid K
corresponding to amino acid 71 of Z36249_PEA.sub.--3_P3 (SEQ ID
NO:314), a second amino acid sequence being at least 90% homologous
to KKKLEQRSKLENLEDLEIIIQLKKRKKYRKTKVPVVKEPEPEIITEPVDVPTFLKAALENK
LPVVEKFLSDKNNPDVCDEYKRTALHRACLEGHLAIVEKLMEAGAQIEFRDM corresponding
to amino acids 72-184 of Q15327 (SEQ ID NO:345), which also
corresponds to amino acids 72-184 of Z36249_PEA.sub.--3_P3 (SEQ ID
NO:314), and a third amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence VNIFLCLGMSQKK (SEQ ID NO:421)
corresponding to amino acids 185-197 of Z36249_PEA.sub.--3_P3 (SEQ
ID NO:314), wherein said first amino acid sequence, bridging amino
acid, second amino acid sequence and third amino acid sequence are
contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
Z36249_PEA.sub.--3_P3 (SEQ ID NO:314), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VNIFLCLGMSQKK (SEQ ID NO:421) in Z36249_PEA.sub.--3_P3 (SEQ ID
NO:314).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein Z36249_PEA.sub.--3_P3 (SEQ ID NO:314) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 6, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein Z36249_PEA.sub.--3_P3 (SEQ ID
NO:314) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00280 TABLE 6 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
34 E -> * Yes
Variant protein Z36249_PEA.sub.--3_P3 (SEQ ID NO:314) is encoded by
the following transcript(s): Z36249_PEA.sub.--3_T3 (SEQ ID NO:39),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript Z36249_PEA 3_T3 (SEQ
ID NO:39) is shown in bold; this coding portion starts at position
250 and ends at position 840. The transcript also has the following
SNPs as listed in Table 7 (given according to their position on the
nucleotide sequence, with the alternative nucleic acid listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein Z36249_PEA.sub.--3_P3 (SEQ ID
NO:314) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00281 TABLE 7 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
105 T -> C Yes 208 T -> .sup. No 349 G -> T Yes 459 C
-> A No
Variant protein Z36249_PEA.sub.--3_P4 (SEQ ID NO:315) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z36249_PEA.sub.--3_T5 (SEQ ID NO:40). One or more alignments to one
or more previously published protein sequences are given at the end
of the application. A brief description of the relationship of the
variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between Z36249_PEA.sub.--3_P4 (SEQ ID NO:315) and
Q96LE7 (SEQ ID NO:344):
1. An isolated chimeric polypeptide encoding for
Z36249_PEA.sub.--3_P4 (SEQ ID NO:315), comprising a first amino
acid sequence being at least 90% homologous to
MMVLKVEELVTGKKNGNGEAGEFLPEDFRDGEYEAAVTLEKQEDLKTLLAHPVTLGE
QQWKSEKQREAELKKKKLEQRSKLENLEDLEIIIQLKKRKKYRKTKVPVVKEPEPEIITE
PVDVPTFLKAALENKLPVVEKFLSDKNNPDVCDE corresponding to amino acids
1-151 of Q96LE7 (SEQ ID NO:344), which also corresponds to amino
acids 1-151 of Z36249_PEA.sub.--3_P4 (SEQ ID NO:315), and a second
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence VRLMQSTAKSSSLILCFLCFTPVLLI (SEQ ID NO:422) corresponding
to amino acids 152-177 of Z36249_PEA.sub.--3_P4 (SEQ ID NO:315),
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
Z36249_PEA.sub.--3_P4 (SEQ ID NO:315), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VRLMQSTAKSSSLILCFLCFTPVLLI (SEQ ID NO:422) in Z36249_PEA.sub.--3_P4
(SEQ ID NO:315).
Comparison report between Z36249_PEA.sub.--3_P4 (SEQ ID NO:315) and
Q15327 (SEQ ID NO:345):
1. An isolated chimeric polypeptide encoding for
Z36249_PEA.sub.--3_P4 (SEQ ID NO:315), comprising a first amino
acid sequence being at least 90% homologous to
MMVLKVEELVTGKKNGNGEAGEFLPEDFRDGEYEAAVTLEKQEDLKTLLAHPVTLGE
QQWKSEKQREAEL corresponding to amino acids 1-70 of Q15327 (SEQ ID
NO:345), which also corresponds to amino acids 1-70 of
Z36249_PEA.sub.--3_P4 (SEQ ID NO:315), a bridging amino acid K
corresponding to amino acid 71 of Z36249_PEA.sub.--3_P4 (SEQ ID
NO:315), a second amino acid sequence being at least 90% homologous
to KKKLEQRSKLENLEDLEIIIQLKKRKKYRKTKVPVVKEPEPEIITEPVDVPTFLKAALENK
LPVVEKFLSDKNNPDVCDE corresponding to amino acids 72-151 of Q15327
(SEQ ID NO:345), which also corresponds to amino acids 72-151 of
Z36249_PEA.sub.--3_P4 (SEQ ID NO:315), and a third amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
VRLMQSTAKSSSLILCFLCFTPVLLI (SEQ ID NO:422) corresponding to amino
acids 152-177 of Z36249_PEA.sub.--3_P4 (SEQ ID NO:315), wherein
said first amino acid sequence, bridging amino acid, second amino
acid sequence and third amino acid sequence are contiguous and in a
sequential order.
2. An isolated polypeptide encoding for a tail of
Z36249_PEA.sub.--3_P4 (SEQ ID NO:315), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VRLMQSTAKSSSLILCFLCFTPVLLI (SEQ ID NO:422) in Z36249_PEA.sub.--3_P4
(SEQ ID NO:315).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because only one of the two trans-membrane
region prediction programs (Tmpred: 1, Tmhmm: 0) has predicted that
this protein has a trans-membrane region. In addition both
signal-peptide prediction programs predict that this protein is a
non-secreted protein.
Variant protein Z36249_PEA.sub.--3_P4 (SEQ ID NO:315) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 8, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein Z36249_PEA.sub.--3_P4 (SEQ ID
NO:315) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00282 TABLE 8 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
34 E -> * Yes
Variant protein Z36249_PEA.sub.--3_P4 (SEQ ID NO:315) is encoded by
the following transcript(s): Z36249_PEA.sub.--3_T5 (SEQ ID NO:40),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript Z36249_PEA.sub.--3_T5
(SEQ ID NO:40) is shown in bold; this coding portion starts at
position 250 and ends at position 780. The transcript also has the
following SNPs as listed in Table 9 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
Z36249_PEA.sub.--3_P4 (SEQ ID NO:315) sequence provides support for
the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00283 TABLE 9 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
105 T -> C Yes 208 T -> .sup. No 349 G -> T Yes 459 C
-> A No 1265 T -> C Yes
Variant protein Z36249_PEA.sub.--3_P5 (SEQ ID NO:316) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z36249_PEA.sub.--3_T9 (SEQ ID NO:41). One or more alignments to one
or more previously published protein sequences are given at the end
of the application. A brief description of the relationship of the
variant protein according to the present invention to each such
aligned protein is as follows:
Comparison report between Z36249_PEA.sub.--3_P5 (SEQ ID NO:316) and
Q96LE7 (SEQ ID NO:344):
1. An isolated chimeric polypeptide encoding for
Z36249_PEA.sub.--3_P5 (SEQ ID NO:316), comprising a first amino
acid sequence being at least 90% homologous to
MMVLKVEELVTGKKNGNGEAGEFLPEDFRDGEYEAAVTLEKQEDLKTLLAHPVTLGE
QQWKSEKQREAELKKKKLEQRSKLENLEDLEIIIQLKKRKKYRKTKVPVVKEPEPEIITE
PVDVPTFLKAALENKLPVVEKFLSDKNNPDVCDE corresponding to amino acids
1-151 of Q96LE7 (SEQ ID NO:344), which also corresponds to amino
acids 1-151 of Z36249_PEA.sub.--3_P5 (SEQ ID NO:316), and a second
amino acid sequence being at least 90% homologous to
LESTAIHWASRGGNLDVLKLLLNKGAKISARDKLLSTALHVAVRTGHYECAEHLIACE
ADLNAKDREGDTPLHDAVRLNRYKMIRLLIMYGADLNIKNCAGKTPMDLVLHWQNG
TKAIFDSLRENSYKTSRIATF corresponding to amino acids 185-319 of
Q96LE7 (SEQ ID NO:344), which also corresponds to amino acids
152-286 of Z36249_PEA.sub.--3_P5 (SEQ ID NO:316), wherein said
first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
2. An isolated chimeric polypeptide encoding for an edge portion of
Z36249_PEA.sub.--3_P5 (SEQ ID NO:316), comprising a polypeptide
having a length "n", wherein n is at least about 10 amino acids in
length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably
at least about 40 amino acids in length and most preferably at
least about 50 amino acids in length, wherein at least two amino
acids comprise EL, having a structure as follows: a sequence
starting from any of amino acid numbers 151-x to 151; and ending at
any of amino acid numbers 152+((n-2)-x), in which x varies from 0
to n-2.
Comparison report between Z36249_PEA.sub.--3_P5 (SEQ ID NO:316) and
Q15327 (SEQ ID NO:345):
1. An isolated chimeric polypeptide encoding for
Z36249_PEA.sub.--3_P5 (SEQ ID NO:316), comprising a first amino
acid sequence being at least 90% homologous to
MMVLKVEELVTGKKNGNGEAGEFLPEDFRDGEYEAAVTLEKQEDLKTLLAHPVTLGE
QQWKSEKQREAEL corresponding to amino acids 1-70 of Q15327 (SEQ ID
NO:345), which also corresponds to amino acids 1-70 of
Z36249_PEA.sub.--3_P5 (SEQ ID NO:316), a bridging amino acid K
corresponding to amino acid 71 of Z36249_PEA.sub.--3_P5 (SEQ ID
NO:316), a second amino acid sequence being at least 90% homologous
to KKKLEQRSKLENLEDLEIIIQLKKRKKYRKTKVPVVKEPEPEIITEPVDVPTFLKAALENK
LPVVEKFLSDKNNPDVCDE corresponding to amino acids 72-151 of Q15327
(SEQ ID NO:345), which also corresponds to amino acids 72-151 of
Z36249_PEA.sub.--3_P5 (SEQ ID NO:316), and a third amino acid
sequence being at least 90% homologous to
BESTAIHWASRGGNLDVLKLLLNKGAKISARDKLLSTALHVAVRTGHYECAEHLIACE
ADLNAKDREGDTPLHDAVRLNRYKMIRLLIMYGADLNIKNCAGKTPMDLVLHWQNG
TKAIFDSLRENSYKTSRIATF corresponding to amino acids 185-319 of
Q15327 (SEQ ID NO:345), which also corresponds to amino acids
152-286 of Z36249_PEA.sub.--3_P5 (SEQ ID NO:316), wherein said
first amino acid sequence, bridging amino acid, second amino acid
sequence and third amino acid sequence are contiguous and in a
sequential order.
2. An isolated chimeric polypeptide encoding for an edge portion of
Z36249_PEA.sub.--3_P5 (SEQ ID NO:316), comprising a polypeptide
having a length "n", wherein n is at least about 10 amino acids in
length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably
at least about 40 amino acids in length and most preferably at
least about 50 amino acids in length, wherein at least two amino
acids comprise EL, having a structure as follows: a sequence
starting from any of amino acid numbers 151-x to 151; and ending at
any of amino acid numbers 152+((n-2)-x), in which x varies from 0
to n-2.
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell:
intracellularly. The protein localization is believed to be
intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein Z36249_PEA.sub.--3_P5 (SEQ ID NO:316) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 10, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein Z36249_PEA.sub.--3_P5 (SEQ ID
NO:316) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00284 TABLE 10 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
34 E -> * Yes
Variant protein Z36249_PEA.sub.--3_P5 (SEQ ID NO:316) is encoded by
the following transcript(s): Z36249_PEA.sub.--3_T9 (SEQ ID NO:41),
for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript Z36249_PEA.sub.--3_T9
(SEQ ID NO:41) is shown in bold; this coding portion starts at
position 250 and ends at position 1107. The transcript also has the
following SNPs as listed in Table 11 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
Z36249_PEA.sub.--3_P5 (SEQ ID NO:316) sequence provides support for
the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00285 TABLE 11 Nucleic acid SNPs SNP position on
nucleotide Alternative Previously sequence nucleic acid known SNP?
105 T -> C Yes 208 T -> .sup. No 349 G -> T Yes 459 C
-> A No 1169 A -> G Yes 1365 C -> T Yes 1426 C -> T Yes
1525 C -> T Yes 1610 C -> T Yes 1714 G -> A Yes 1770 G
-> A Yes
As noted above, cluster Z36249 features 11 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster Z36249_PEA.sub.--3_node.sub.--0 (SEQ ID NO:186)
according to the present invention is supported by 42 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T2 (SEQ ID NO:38), Z36249_PEA.sub.--3_T3 (SEQ ID
NO:39), Z36249_PEA.sub.--3_T5 (SEQ ID NO:40) and
Z36249_PEA.sub.--3_T9 (SEQ ID NO:41). Table 12 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00286 TABLE 12 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T2 (SEQ ID NO: 38) 1 276 Z36249_PEA_3_T3 (SEQ ID NO:
39) 1 276 Z36249_PEA_3_T5 (SEQ ID NO: 40) 1 276 Z36249_PEA_3_T9
(SEQ ID NO: 41) 1 276
Segment cluster Z36249_PEA.sub.--3_node.sub.--3 (SEQ ID NO:187)
according to the present invention is supported by 45 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T2 (SEQ ID NO:38), Z36249_PEA.sub.--3_T3 (SEQ ID
NO:39), Z36249_PEA.sub.--3_T5 (SEQ ID NO:40) and
Z36249_PEA.sub.--3_T9 (SEQ ID NO:41). Table 13 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00287 TABLE 13 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T2 (SEQ ID NO: 38) 277 456 Z36249_PEA_3_T3 (SEQ ID NO:
39) 277 456 Z36249_PEA_3_T5 (SEQ ID NO: 40) 277 456 Z36249_PEA_3_T9
(SEQ ID NO: 41) 277 456
Segment cluster Z36249_PEA.sub.--3_node.sub.--5 (SEQ ID NO:188)
according to the present invention is supported by 34 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T2 (SEQ ID NO:38), Z36249_PEA.sub.--3_T3 (SEQ ID
NO:39), Z36249_PEA.sub.--3_T5 (SEQ ID NO:40) and
Z36249_PEA.sub.--3_T9 (SEQ ID NO:41). Table 14 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00288 TABLE 14 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T2 (SEQ ID NO: 38) 457 594 Z36249_PEA_3_T3 (SEQ ID NO:
39) 457 594 Z36249_PEA_3_T5 (SEQ ID NO: 40) 457 594 Z36249_PEA_3_T9
(SEQ ID NO: 41) 457 594
Segment cluster Z36249_PEA.sub.--3_node.sub.--11 (SEQ ID NO:189)
according to the present invention is supported by 4 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T5 (SEQ ID NO:40). Table 15 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00289 TABLE 15 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T5 (SEQ ID NO: 40) 703 1387
Segment cluster Z36249_PEA.sub.--3_node.sub.--14 (SEQ ID NO:190)
according to the present invention is supported by 5 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T3 (SEQ ID NO:39). Table 16 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00290 TABLE 16 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T3 (SEQ ID NO: 39) 802 1472
Segment cluster Z36249_PEA.sub.--3_node.sub.--24 (SEQ ID NO:191)
according to the present invention is supported by 34 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T2 (SEQ ID NO:38) and Z36249_PEA.sub.--3_T9 (SEQ
ID NO:41). Table 17 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00291 TABLE 17 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T2 (SEQ ID NO: 38) 991 2064 Z36249_PEA_3_T9 (SEQ ID
NO: 41) 1000 1877
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster Z36249_PEA.sub.--3_node.sub.--10 (SEQ ID NO:192)
according to the present invention is supported by 30 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T3 (SEQ ID NO:39), Z36249_PEA.sub.--3_T5 (SEQ ID
NO:40) and Z36249_PEA.sub.--3_T9 (SEQ ID NO:41). Table 18 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00292 TABLE 18 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T3 (SEQ ID NO: 39) 595 702 Z36249_PEA_3_T5 (SEQ ID NO:
40) 595 702 Z36249_PEA_3_T9 (SEQ ID NO: 41) 595 702
Segment cluster Z36249_PEA.sub.--3_node.sub.--13 (SEQ ID NO:193)
according to the present invention is supported by 29 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T2 (SEQ ID NO:38) and Z36249_PEA.sub.--3_T3 (SEQ
ID NO:39). Table 19 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00293 TABLE 19 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T2 (SEQ ID NO: 38) 595 693 Z36249_PEA_3_T3 (SEQ ID NO:
39) 703 801
Segment cluster Z36249_PEA.sub.--3_node.sub.--17 (SEQ ID NO:194)
according to the present invention is supported by 26 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T2 (SEQ ID NO:38) and Z36249_PEA.sub.--3_T9 (SEQ
ID NO:41). Table 20 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00294 TABLE 20 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T2 (SEQ ID NO: 38) 694 792 Z36249_PEA_3_T9 (SEQ ID NO:
41) 703 801
Segment cluster Z36249_PEA.sub.--3_node.sub.--19 (SEQ ID NO:195)
according to the present invention is supported by 24 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T2 (SEQ ID NO:38) and Z36249_PEA.sub.--3_T9 (SEQ
ID NO:41). Table 21 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00295 TABLE 21 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T2 (SEQ ID NO: 38) 793 891 Z36249_PEA_3_T9 (SEQ ID NO:
41) 802 900
Segment cluster Z36249_PEA.sub.--3_node.sub.--21 (SEQ ID NO:196)
according to the present invention is supported by 18 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z36249_PEA.sub.--3_T2 (SEQ ID NO:38) and Z36249_PEA.sub.--3_T9 (SEQ
ID NO:41). Table 22 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00296 TABLE 22 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z36249_PEA_3_T2 (SEQ ID NO: 38) 892 990 Z36249_PEA_3_T9 (SEQ ID NO:
41) 901 999
Variant Protein Alignment to the Previously Known Protein: Sequence
name: Q96LE7 (SEQ ID NO:344) Sequence documentation: Alignment of:
Z36249_PEA3_P2 (SEQ ID NO:313)+Q96LE7 (SEQ ID NO:344).
TABLE-US-00297 Alignment segment 1/1: Quality: 2639.00 Escore: 0
Matching length: 283 Total length: 319 Matching Percent Similarity:
100.00 Matching Percent 100.00 Identity: Total Percent Similarity:
88.71 Total Percent Identity: 88.71 Gaps: 1
Alignment:
##STR00039## Sequence name: Q15327 (SEQ ID NO:345) Sequence
documentation: Alignment of: Z36249_PEA.sub.--3_P2 (SEQ ID
NO:313)+Q15327 (SEQ ID NO:345).
TABLE-US-00298 Alignment segment 1/1: Quality: 2626.00 Escore: 0
Matching length: 283 Total length: 319 Matching Percent Similarity:
99.65 Matching Percent 99.65 Identity: Total Percent Similarity:
88.40 Total Percent Identity: 88.40 Gaps: 1
Alignment:
##STR00040## Sequence name: Q96LE7 (SEQ ID NO:344) Sequence
documentation: Alignment of: Z36249_PEA.sub.--3_P3 (SEQ ID
NO:344)+Q96LE7 (SEQ ID NO:344).
TABLE-US-00299 Alignment segment 1/1: Quality: 1785.00 Escore: 0
Matching length: 184 Total length: 184 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00041## Sequence name: Q15327 (SEQ ID NO:345) Sequence
documentation: Alignment of: Z35249_PEA.sub.--3_P3 (SEQ ID
NO:314)+Q15327 (SEQ ID NO:345).
TABLE-US-00300 Alignment segment 1/1: Quality: 1772.00 Escore: 0
Matching length: 184 Total length: 184 Matching Percent 99.46
Matching Percent Identity: 99.46 Similarity: Total Percent
Similarity: 99.46 Total Percent Identity: 99.46 Gaps: 0
Alignment:
##STR00042## Sequence name: Q96LE7 (SEQ ID NO:344) Sequence
documentation: Alignment of: Z36249_PEA.sub.--3_P4 (SEQ ID
NO:315)+Q96LE7 (SEQ ID NO:344).
TABLE-US-00301 Alignment segment 1/1: Quality: 1464.00 Escore: 0
Matching length: 151 Total length: 151 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00043## Sequence name: Q15327 (SEQ ID NO:345) Sequence
documentation: Alignment of: Z36249_PEA.sub.--3_P4 (SEQ ID
NO:315)+Q15327 (SEQ ID NO:345).
TABLE-US-00302 Alignment segment 1/1: Quality: 1451.00 Escore: 0
Matching length: 151 Total length: 151 Matching Percent 99.34
Matching Percent Identity: 99.34 Similarity: Total Percent
Similarity: 99.34 Total Percent Identity: 99.34 Gaps: 0
Alignment:
##STR00044## Sequence name: Q96LE7 (SEQ ID NO:344) Sequence
documentation: Alignment of: Z36249_PEA.sub.--3_P5 (SEQ ID
NO:316)+Q96LE7 (SEQ ID NO:344).
TABLE-US-00303 Alignment segment 1/1: Quality: 2670.00 Escore: 0
Matching length: 286 Total length: 319 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 89.66 Total Percent Identity: 89.66 Gaps: 1
Alignment:
##STR00045## Sequence name: Q15327 (SEQ ID NO:345) Sequence
documentation: Alignment of: Z36249_PEA.sub.--3_P5 (SEQ ID
NO:316)+Q15327 (SEQ ID NO:345).
TABLE-US-00304 Alignment segment 1/1: Quality: 2657.00 Escore: 0
Matching length: 286 Total length: 319 Matching Percent 99.65
Matching Percent Identity: 99.65 Similarity: Total Percent
Similarity: 89.34 Total Percent Identity: 89.34 Gaps: 1
Alignment:
##STR00046##
Description for Cluster Z25377
Cluster Z25377 features 9 transcript(s) and 12 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00305 TABLE 1 Transcripts of interest Transcript Name Seq
ID No. Z25377_PEA_1_T1 42 Z25377_PEA_1_T5 43 Z25377_PEA_1_T7 44
Z25377_PEA_1_T8 45 Z25377_PEA_1_T9 46 Z25377_PEA_1_T10 47
Z25377_PEA_1_T11 48 Z25377_PEA_1_T12 49 Z25377_PEA_1_T13 50
TABLE-US-00306 TABLE 2 Segments of interest Segment Name Seq ID No.
Z25377_PEA_1_node_5 197 Z25377_PEA_1_node_12 198
Z25377_PEA_1_node_15 199 Z25377_PEA_1_node_17 200
Z25377_PEA_1_node_18 201 Z25377_PEA_1_node_22 202
Z25377_PEA_1_node_24 203 Z25377_PEA_1_node_0 204
Z25377_PEA_1_node_7 205 Z25377_PEA_1_node_8 206
Z25377_PEA_1_node_10 207 Z25377_PEA_1_node_20 208
TABLE-US-00307 TABLE 3 Proteins of interest Protein Name Seq ID No.
Corresponding Transcript(s) Z25377_PEA_1_P12 317 Z25377_PEA_1_T11
(SEQ ID NO: 48) Z25377_PEA_1_P13 318 Z25377_PEA_1_T12 (SEQ ID NO:
49) Z25377_PEA_1_P14 319 Z25377_PEA_1_T13 (SEQ ID NO: 50)
Z25377_PEA_1_P15 320 Z25377_PEA_1_T1 (SEQ ID NO: 42)
Z25377_PEA_1_P17 321 Z25377_PEA_1_T5 (SEQ ID NO: 43)
Z25377_PEA_1_P18 322 Z25377_PEA_1_T7 (SEQ ID NO: 44)
Z25377_PEA_1_P19 323 Z25377_PEA_1_T8 (SEQ ID NO: 45)
Z25377_PEA_1_P20 324 Z25377_PEA_1_T9 (SEQ ID NO: 46)
Z25377_PEA_1_P21 325 Z25377_PEA_1_T10 (SEQ ID NO: 47)
These sequences are variants of the known protein Hypothetical
protein FLJ26352 (SEQ ID NO:390) (SwissProt accession identifier
Q6ZP80; known also according to the synonyms RLN16974), referred to
herein as the previously known protein.
The sequence for protein Hypothetical protein FLJ26352 is given at
the end of the application, as "Hypothetical protein FLJ26352 amino
acid sequence" (SEQ ID NO:390).
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster Z25377. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 29 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 29, concerning the number of
heart-specific clones in libraries/sequences.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs, which was found to be 13.3; the ratio of
expression of the cluster in heart specific ESTs to the overall
expression of the cluster in muscle-specific ESTs which was found
to be 4.9; and fisher exact test P-values were computed both for
library and weighted clone counts to check that the counts are
statistically significant, and were found to be 6.50E-07.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the ratio of expression of the cluster
in heart specific ESTs to the overall expression of the cluster in
muscle-specific ESTs which was found to be 13.3, which clearly
supports specific expression in heart tissue.
As noted above, cluster Z25377 features 9 transcript(s), which were
listed in Table 1 above. These transcript(s) encode for protein(s)
which are variant(s) of protein Hypothetical protein FLJ26352 (SEQ
ID NO:390). A description of each variant protein according to the
present invention is now provided.
Variant protein Z25377_PEA.sub.--1_P12 (SEQ ID NO:317) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z25377_PEA.sub.--1_T11 (SEQ ID NO:48). An alignment is given to the
known protein (Hypothetical protein FLJ26352 (SEQ ID NO:390)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between Z25377_PEA.sub.--1_P12 (SEQ ID NO:317)
and BAC85244 (SEQ ID NO:341):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P12 (SEQ ID NO:317), comprising a first amino
acid sequence being at least 90% homologous to
MRLNIAIFFGALFGALGVLLFLVAFGSDYWLLATEVGRCSGEKNIENVTFHHEGFFWRC
WFNGIVEENDSNIWKFWYTNQPPSKNCTHAYLSPYPFMRGEHNSTSYDSAVIYRGFWA
VLMLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIAAGI corresponding to amino
acids 1-158 of BAC85244 (SEQ ID NO:341), which also corresponds to
amino acids 1-158 of Z25377_PEA.sub.--1_P12 (SEQ ID NO:317).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: membrane. The protein localization is believed to be
membrane because although both signal-peptide prediction programs
agree that this protein has a signal peptide, both trans-membrane
region prediction programs predict that this protein has a
trans-membrane region downstream of this signal peptide.
Variant protein Z25377_PEA.sub.--1_P12 (SEQ ID NO:317) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 4, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein Z25377_PEA.sub.--1_P12 (SEQ ID
NO:317) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00308 TABLE 4 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
157 G -> E No
Variant protein Z25377_PEA.sub.--1_P12 (SEQ ID NO:317) is encoded
by the following transcript(s): Z25377_PEA.sub.--1_T11 (SEQ ID
NO:48), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
Z25377_PEA.sub.--1_T11 (SEQ ID NO:48) is shown in bold; this coding
portion starts at position 188 and ends at position 661. The
transcript also has the following SNPs as listed in Table 5 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein Z25377_PEA.sub.--1_P12 (SEQ ID NO:317) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00309 TABLE 5 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
71 T -> C Yes 99 T -> .sup. Yes 657 G -> A No 933 T ->
.sup. No 935 T -> A No
Variant protein Z25377_PEA.sub.--1_P13 (SEQ ID NO:318) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z25377_PEA.sub.--1_T12 (SEQ ID NO:49). An alignment is given to the
known protein (Hypothetical protein FLJ26352 (SEQ ID NO:390)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between Z25377_PEA.sub.--1_P13 (SEQ ID NO:318)
and BAC85244 (SEQ ID NO:341):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P13 (SEQ ID NO:318), comprising a first amino
acid sequence being at least 90% homologous to
MRLNIAIFFGALFGALGVLLFLVAFGSDYWLLATEVGRCSGEKNIENVTFHHEGFFWRC
WFNGIVEENDSNIWKFWYTNQPPSKNCTHAYLSPYPFMRGEHNSTSYDSAVIYRGFWA
VLMLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIAA corresponding to amino
acids 1-156 of BAC85244 (SEQ ID NO:341), which also corresponds to
amino acids 1-156 of Z25377_PEA.sub.--1_P13 (SEQ ID NO:318), and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence VSVGQECGSG (SEQ ID NO:423) corresponding to amino acids
157-166 of Z25377_PEA.sub.--1_P13 (SEQ ID NO:318), wherein said
first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
Z25377_PEA.sub.--1.sub.13 P13 (SEQ ID NO:318), comprising a
polypeptide being at least 70%, optionally at least about 80%,
preferably at least about 85%, more preferably at least about 90%
and most preferably at least about 95% homologous to the sequence
VSVGQECGSG (SEQ ID NO:423) in Z25377_PEA.sub.--1_P13 (SEQ ID
NO:318).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: membrane. The protein localization is believed to be
membrane because although both signal-peptide prediction programs
agree that this protein has a signal peptide, both trans-membrane
region prediction programs predict that this protein has a
trans-membrane region downstream of this signal peptide.
Variant protein Z25377_PEA.sub.--1_P13 (SEQ ID NO:318) is encoded
by the following transcript(s): Z25377_PEA.sub.--1_T12 (SEQ ID
NO:49), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
Z25377_PEA.sub.--1_T12 (SEQ ID NO:49) is shown in bold; this coding
portion starts at position 188 and ends at position 685. The
transcript also has the following SNPs as listed in Table 6 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein Z25377_PEA.sub.--1_P13 (SEQ ID NO:318) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00310 TABLE 6 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
71 T -> C Yes 99 T -> .sup. Yes
Variant protein Z25377_PEA.sub.--1_P14 (SEQ ID NO:319) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z25377_PEA.sub.--1_T13 (SEQ ID NO:50). An alignment is given to the
known protein (Hypothetical protein FLJ26352 (SEQ ID NO:390)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between Z25377_PEA.sub.--1_P14 (SEQ ID NO:319)
and BAC85244 (SEQ ID NO:341):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P14 (SEQ ID NO:319), comprising a first amino
acid sequence being at least 90% homologous to
MRLNIAIFFGALFGALGVLLFLVAFGSDYWLLATEVGRCSGEKNIENVTFHHEGFFWRC
WFNGIVEENDSNIWKFWYTNQPPSKNCTHAYLSPYPFMRGEHNSTSYDSAVIYRGFWA
VLMLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIAA corresponding to amino
acids 1-156 of BAC85244 (SEQ ID NO:341), which also corresponds to
amino acids 1-156 of Z25377_PEA.sub.--1_P14 (SEQ ID NO:319), and a
second amino acid sequence being at least 70%, optionally at least
80%, preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence DGISSLCYSSLSKSLLSQPLRETSSAINDISLLQALMPLLGWTSHWTCITVGLY
(SEQ ID NO:424) corresponding to amino acids 157-210 of
Z25377_PEA.sub.--1_P14 (SEQ ID NO:319), wherein said first amino
acid sequence and second amino acid sequence are contiguous and in
a sequential order.
2. An isolated polypeptide encoding for a tail of
Z25377_PEA.sub.--1_P14 (SEQ ID NO:319), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
DGISSLCYSSLSKSLLSQPLRETSSAINDISLLQALMPLLGWTSHWTCITVGLY (SEQ ID
NO:424) in Z25377_PEA.sub.--1_P14 (SEQ ID NO:319).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: membrane. The protein localization is believed to be
membrane because although both signal-peptide prediction programs
agree that this protein has a signal peptide, both trans-membrane
region prediction programs predict that this protein has a
trans-membrane region downstream of this signal peptide.
Variant protein Z25377_PEA.sub.--1_P14 (SEQ ID NO:319) is encoded
by the following transcript(s): Z25377_PEA.sub.--1_T13 (SEQ ID
NO:50), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
Z25377_PEA.sub.--1_T13 (SEQ ID NO:50) is shown in bold; this coding
portion starts at position 188 and ends at position 817. The
transcript also has the following SNPs as listed in Table 7 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein Z25377_PEA.sub.--1_P14 (SEQ ID NO:319) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00311 TABLE 7 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
71 T -> C Yes 99 T -> .sup. Yes 823 T -> .sup. No 825 T
-> A No
Variant protein Z25377_PEA.sub.--1_P15 (SEQ ID NO:320) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z25377_PEA.sub.--1_T1 (SEQ ID NO:42). An alignment is given to the
known protein (Hypothetical protein FLJ26352 (SEQ ID NO:390)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between Z25377_PEA.sub.--1_P15 (SEQ ID NO:320)
and Q96NR4 (SEQ ID NO:342):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P15 (SEQ ID NO:320), comprising a first amino
acid sequence being at least 90% homologous to
MRGEHNSTSYDSAVIYRGFWAVLMLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIA A
corresponding to amino acids 1-60 of Q96NR4 (SEQ ID NO:342), which
also corresponds to amino acids 1-60 of Z25377_PEA.sub.--1_P15 (SEQ
ID NO:320), and a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence
DGISSLCYSSLSKSLLSQPLRETSSAINDISLLQALMPLLGWTSHWTCITVGLY (SEQ ID
NO:424) corresponding to amino acids 61-114 of
Z25377_PEA.sub.--1_P15 (SEQ ID NO:320), wherein said first amino
acid sequence and second amino acid sequence are contiguous and in
a sequential order.
2. An isolated polypeptide encoding for a tail of
Z25377_PEA.sub.--1_P15 (SEQ ID NO:320), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
DGISSLCYSSLSKSLLSQPLRETSSAINDISLLQALMPLLGWTSHWTCITVGLY (SEQ ID
NO:424) in Z25377_PEA.sub.--1_P15 (SEQ ID NO:320).
Comparison report between Z25377_PEA.sub.--1_P15 (SEQ ID NO:320)
and BAC85244 (SEQ ID NO:341):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P15 (SEQ ID NO:320), comprising a first amino
acid sequence being at least 90% homologous to
MRGEHNSTSYDSAVIYRGFWAVLMLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIA A
corresponding to amino acids 97-156 of BAC85244 (SEQ ID NO:341),
which also corresponds to amino acids 1-60 of
Z25377_PEA.sub.--1_P15 (SEQ ID NO:320), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
DGISSLCYSSLSKSLLSQPLRETSSAINDISLLQALMPLLGWTSHWTCITVGLY (SEQ ID
NO:424) corresponding to amino acids 61-114 of
Z25377_PEA.sub.--1_P15 (SEQ ID NO:320), wherein said first amino
acid sequence and second amino acid sequence are contiguous and in
a sequential order.
2. An isolated polypeptide encoding for a tail of
Z25377_PEA.sub.--1_P15 (SEQ ID NO:320), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
DGISSLCYSSLSKSLLSQPLRETSSAINDISLLQALMPLLGWTSHWTCITVGLY (SEQ ID
NO:424) in Z25377_PEA.sub.--1_P15 (SEQ ID NO:320).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: membrane. The protein localization is believed to be
membrane because the Signalp_hmm software predicts that this
protein has a signal anchor region.
Variant protein Z25377_PEA.sub.--1_P15 (SEQ ID NO:320) is encoded
by the following transcript(s): Z25377_PEA.sub.--1_T1 (SEQ ID
NO:42), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript Z25377_PEA.sub.--1_T1
(SEQ ID NO:42) is shown in bold; this coding portion starts at
position 261 and ends at position 602. The transcript also has the
following SNPs as listed in Table 8 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
Z25377_PEA.sub.--1_P15 (SEQ ID NO:320) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00312 TABLE 8 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
608 T -> No 610 T -> A No
Variant protein Z25377_PEA.sub.--1_P17 (SEQ ID NO:321) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z25377_PEA.sub.--1_T5 (SEQ ID NO:43). An alignment is given to the
known protein (Hypothetical protein FLJ26352 (SEQ ID NO:390)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between Z25377_PEA.sub.--1_P17 (SEQ ID NO:321)
and Q96NR4 (SEQ ID NO:342):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), comprising a first amino
acid sequence being at least 90% homologous to MRGEHNSTSYDSAV
corresponding to amino acids 1-14 of Q96NR4 (SEQ ID NO:342), which
also corresponds to amino acids 1-14 of Z25377_PEA.sub.--1_P17 (SEQ
ID NO:321), a second amino acid sequence bridging amino acid
sequence comprising of S, and a third amino acid sequence being at
least 90% homologous to
ILFSLVVMLYVIWVQAVADMESYRNMKMKDCLDFTPSVLYGWSFFLAPAGIFFSLLAG
LLFLVVGRHIQIHH corresponding to amino acids 62-133 of Q96NR4 (SEQ
ID NO:342), which also corresponds to amino acids 16-87 of
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), wherein said first amino
acid sequence, second amino acid sequence and third amino acid
sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for an edge portion of
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), comprising a polypeptide
having a length "n", wherein n is at least about 10 amino acids in
length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably
at least about 40 amino acids in length and most preferably at
least about 50 amino acids in length, wherein at least two amino
acids comprise VSI having a structure as follows (numbering
according to Z25377_PEA.sub.--1_P17 (SEQ ID NO:321)): a sequence
starting from any of amino acid numbers 14-x to 14; and ending at
any of amino acid numbers 16+((n-2)-x), in which x varies from 0 to
n-2.
Comparison report between Z25377_PEA.sub.--1_P17 (SEQ ID NO:321)
and Q8WW45 (SEQ ID NO:343):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), comprising a first amino
acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence MRGEHNSTSYDSAVS (SEQ ID NO:426) corresponding to amino
acids 1-15 of Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), and a second
amino acid sequence being at least 90% homologous to
ILFSLVVMLYVIWVQAVADMESYRNMKMKDCLDFTPSVLYGWSFFLAPAGIFFSLLAG
LLFLVVGRHIQIHH corresponding to amino acids 39-110 of Q8WW45 (SEQ
ID NO:343), which also corresponds to amino acids 16-87 of
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), wherein said first amino
acid sequence and second amino acid sequence are contiguous and in
a sequential order.
2. An isolated polypeptide encoding for a head of
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
MRGEHNSTSYDSAVS (SEQ ID NO:426) of Z25377_PEA.sub.--1_P17 (SEQ ID
NO:321).
Comparison report between Z25377_PEA.sub.--1_P17 (SEQ ID NO:321)
and BAC85244 (SEQ ID NO:341):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), comprising a first amino
acid sequence being at least 90% homologous to MRGEHNSTSYDSAV
corresponding to amino acids 97-110 of BAC85244 (SEQ ID NO:341),
which also corresponds to amino acids 1-14 of
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), a second amino acid
sequence bridging amino acid sequence comprising of S, and a third
amino acid sequence being at least 90% homologous to
ILFSLVVMLYVIWVQAVADMESYRNMKMKDCLDFTPSVLYGWSFFLAPAGIFFSLLAG
LLFLVVGRHIQIHH corresponding to amino acids 158-229 of BAC85244
(SEQ ID NO:341), which also corresponds to amino acids 16-87 of
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), wherein said first amino
acid sequence, second amino acid sequence and third amino acid
sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for an edge portion of
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321), comprising a polypeptide
having a length "n", wherein n is at least about 10 amino acids in
length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably
at least about 40 amino acids in length and most preferably at
least about 50 amino acids in length, wherein at least two amino
acids comprise
VSI having a structure as follows (numbering according to
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321)): a sequence starting from
any of amino acid numbers 14-x to 14; and ending at any of amino
acid numbers 16+((n-2)-x), in which x varies from 0 to n-2.
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: membrane. The protein localization is believed to be
membrane because although it is a partial protein, because both
trans-membrane region prediction programs predict that this protein
has a trans-membrane region.
Variant protein Z25377_PEA.sub.--1_P17 (SEQ ID NO:321) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 9, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein Z25377_PEA.sub.--1_P17 (SEQ ID
NO:321) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00313 TABLE 9 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
81 R -> W Yes
Variant protein Z25377_PEA.sub.--1_P17 (SEQ ID NO:321) is encoded
by the following transcript(s): Z25377_PEA.sub.--1_T5 (SEQ ID
NO:43), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript Z25377_PEA.sub.--1_T5
(SEQ ID NO:43) is shown in bold; this coding portion starts at
position 261 and ends at position 521. The transcript also has the
following SNPs as listed in Table 10 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
Z25377_PEA.sub.--1_P17 (SEQ ID NO:321) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00314 TABLE 10 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
501 C -> T Yes 1415 T -> C Yes 1434 A -> G Yes 1822 C
-> T Yes 1884 G -> A Yes 2392 C -> G Yes 2454 T -> C No
2618 C -> T Yes 2724 T -> A Yes
Variant protein Z25377_PEA.sub.--1_P18 (SEQ ID NO:322) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z25377_PEA.sub.--1_T7 (SEQ ID NO:44). An alignment is given to the
known protein (Hypothetical protein FLJ26352 (SEQ ID NO:390)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between Z25377_PEA.sub.--1.sub.13 P18 (SEQ ID
NO:322) and Q96NR4 (SEQ ID NO:342):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P18 (SEQ ID NO:322), comprising a first amino
acid sequence being at least 90% homologous to
MRGEHNSTSYDSAVIYRGFWAVLMLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIA AGI
corresponding to amino acids 1-62 of Q96NR4 (SEQ ID NO:342), which
also corresponds to amino acids 1-62 of Z25377_PEA.sub.--1_P18 (SEQ
ID NO:322).
Comparison report between Z25377_PEA.sub.--1_P18 (SEQ ID NO:322)
and Q8WW45 (SEQ ID NO:343):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1.sub.13 P18 (SEQ ID NO:322), comprising a first
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence MRGEHNSTSYDSAVIYRGFWAVL (SEQ ID NO:427) corresponding to
amino acids 1-23 of Z25377_PEA.sub.--1_P18 (SEQ ID NO:322), and a
second amino acid sequence being at least 90% homologous to
MLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIAAGI corresponding to amino
acids 1-39 of Q8WW45 (SEQ ID NO:343), which also corresponds to
amino acids 24-62 of Z25377_PEA.sub.--1_P18 (SEQ ID NO:322),
wherein said first amino acid sequence and second amino acid
sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for a head of
Z25377_PEA.sub.--1_P18 (SEQ ID NO:322), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
MRGEHNSTSYDSAVIYRGFWAVL (SEQ ID NO:427) of Z25377_PEA.sub.--1_P 18
(SEQ ID NO:322).
Comparison report between Z25377_PEA.sub.--1_P18 (SEQ ID NO:322)
and BAC85244 (SEQ ID NO:341):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P18 (SEQ ID NO:322), comprising a first amino
acid sequence being at least 90% homologous to
MRGEHNSTSYDSAVIYRGFWAVLMLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIA AGI
corresponding to amino acids 97-158 of BAC85244 (SEQ ID NO:341),
which also corresponds to amino acids 1-62 of
Z25377_PEA.sub.--1_P18 (SEQ ID NO:322).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: membrane. The protein localization is believed to be
membrane because the Signalp_hmm software predicts that this
protein has a signal anchor region.
Variant protein Z25377_PEA.sub.--1_P18 (SEQ ID NO:322) also has the
following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 11, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein Z25377_PEA.sub.--1_P18 (SEQ ID
NO:322) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00315 TABLE 11 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
61 G -> E No
Variant protein Z25377_PEA.sub.--1_P18 (SEQ ID NO:322) is encoded
by the following transcript(s): Z25377_PEA.sub.--1_T7 (SEQ ID
NO:44), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript Z25377_PEA.sub.--1_T7
(SEQ ID NO:44) is shown in bold; this coding portion starts at
position 261 and ends at position 446. The transcript also has the
following SNPs as listed in Table 12 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
Z25377_PEA.sub.--1_P18 (SEQ ID NO:322) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00316 TABLE 12 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
442 G -> A No 718 T -> No 720 T -> A No
Variant protein Z25377_PEA.sub.--1_P19 (SEQ ID NO:323) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z25377_PEA.sub.--1_T8 (SEQ ID NO:45). The location of the variant
protein was determined according to results from a number of
different software programs and analyses, including analyses from
SignalP and other specialized programs. The variant protein is
believed to be located as follows with regard to the cell:
intracellularly. The protein localization is believed to be
intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein Z25377_PEA.sub.--1_P19 (SEQ ID NO:323) is encoded
by the following transcript(s): Z25377_PEA.sub.--1_T8 (SEQ ID
NO:45), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript Z25377_PEA.sub.--1_T8
(SEQ ID NO:45) is shown in bold; this coding portion starts at
position 127 and ends at position 261. The transcript also has the
following SNPs as listed in Table 13 (given according to their
position on the nucleotide sequence, with the alternative nucleic
acid listed; the last column indicates whether the SNP is known or
not; the presence of known SNPs in variant protein
Z25377_PEA.sub.--1_P19 (SEQ ID NO:323) sequence provides support
for the deduced sequence of this variant protein according to the
present invention).
TABLE-US-00317 TABLE 13 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
354 C -> T Yes 508 A -> G Yes
Variant protein Z25377_PEA.sub.--1_P20 (SEQ ID NO:324) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z25377_PEA.sub.--1_T9 (SEQ ID NO:46). An alignment is given to the
known protein (Hypothetical protein FLJ26352 (SEQ ID NO:390)) at
the end of the application. One or more alignments to one or more
previously published protein sequences are given at the end of the
application. A brief description of the relationship of the variant
protein according to the present invention to each such aligned
protein is as follows:
Comparison report between Z25377_PEA.sub.--1_P20 (SEQ ID NO:324)
and Q96NR4 (SEQ ID NO:342):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), comprising a first amino
acid sequence being at least 90% homologous to
MRGEHNSTSYDSAVIYRGFWAVLMLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIA A
corresponding to amino acids 1-60 of Q96NR4 (SEQ ID NO:342), which
also corresponds to amino acids 1-60 of Z25377_PEA.sub.--1_P20 (SEQ
ID NO:324), and a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence VSVGQECGSG (SEQ ID NO:423)
corresponding to amino acids 61-70 of Z25377_PEA.sub.--1_P20 (SEQ
ID NO:324), wherein said first amino acid sequence and second amino
acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence VSVGQECGSG
(SEQ ID NO:423) in Z25377_PEA.sub.--1_P20 (SEQ ID NO:324).
Comparison report between Z25377_PEA.sub.--1_P20 (SEQ ID NO:324)
and Q8WW45 (SEQ ID NO:343):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), comprising a first amino
acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence MRGEHNSTSYDSAVIYRGFWAVL (SEQ ID NO:427) corresponding to
amino acids 1-23 of Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), a
second amino acid sequence being at least 90% homologous to
MLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIAA corresponding to amino acids
1-37 of Q8WW45 (SEQ ID NO:343), which also corresponds to amino
acids 24-60 of Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), and a third
amino acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence VSVGQECGSG (SEQ ID NO:423) corresponding to amino acids
61-70 of Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), wherein said first
amino acid sequence, second amino acid sequence and third amino
acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for a head of
Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
MRGEHNSTSYDSAVIYRGFWAVL (SEQ ID NO:427) of Z25377_PEA.sub.--1_P20
(SEQ ID NO:324).
3. An isolated polypeptide encoding for a tail of
Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence VSVGQECGSG
(SEQ ID NO:423) in Z25377_PEA.sub.--1_P20 (SEQ ID NO:324).
Comparison report between Z25377_PEA.sub.--1_P20 (SEQ ID NO:324)
and BAC85244 (SEQ ID NO:341):
1. An isolated chimeric polypeptide encoding for
Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), comprising a first amino
acid sequence being at least 90% homologous to
MRGEHNSTSYDSAVIYRGFWAVLMLLGVVAVVIASFLIICAAPFASHFLYKAGGGSYIA A
corresponding to amino acids 97-156 of BAC85244 (SEQ ID NO:341),
which also corresponds to amino acids 1-60 of
Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
VSVGQECGSG (SEQ ID NO:423) corresponding to amino acids 61-70 of
Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), wherein said first amino
acid sequence and second amino acid sequence are contiguous and in
a sequential order.
2. An isolated polypeptide encoding for a tail of
Z25377_PEA.sub.--1_P20 (SEQ ID NO:324), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence VSVGQECGSG
(SEQ ID NO:423) in Z25377_PEA.sub.--1_P20 (SEQ ID NO:324).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: membrane. The protein localization is believed to be
membrane because the Signalp_hmm software predicts that this
protein has a signal anchor region.
Variant protein Z25377_PEA.sub.--1_P20 (SEQ ID NO:324) is encoded
by the following transcript(s): Z25377_PEA.sub.--1_T9 (SEQ ID
NO:46), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript Z25377_PEA.sub.--1_T9
(SEQ ID NO:46) is shown in bold; this coding portion starts at
position 261 and ends at position 470.
Variant protein Z25377_PEA.sub.--1_P21 (SEQ ID NO:325) according to
the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
Z25377_PEA.sub.--1_T10 (SEQ ID NO:47). The location of the variant
protein was determined according to results from a number of
different software programs and analyses, including analyses from
SignalP and other specialized programs. The variant protein is
believed to be located as follows with regard to the cell:
intracellularly. The protein localization is believed to be
intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein Z25377_PEA.sub.--1_P21 (SEQ ID NO:325) is encoded
by the following transcript(s): Z25377_PEA.sub.--1_T10 (SEQ ID
NO:47), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
Z25377_PEA.sub.--1_T10 (SEQ ID NO:47) is shown in bold; this coding
portion starts at position 261 and ends at position 464. The
transcript also has the following SNPs as listed in Table 14 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein Z25377_PEA.sub.--1_P21 (SEQ ID NO:325) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00318 TABLE 14 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
470 T -> No 472 T -> A No
As noted above, cluster Z25377 features 12 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster Z25377_PEA.sub.--1_node.sub.--5 (SEQ ID NO:197)
according to the present invention is supported by 1 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T11(SEQ ID NO:48), Z25377_PEA.sub.--1_T12 (SEQ
ID NO:49) and Z25377_PEA.sub.--1_T13 (SEQ ID NO:50). Table 15 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00319 TABLE 15 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T11 (SEQ ID NO: 48) 1 319 Z25377_PEA_1_T12 (SEQ ID NO:
49) 1 319 Z25377_PEA_1_T13 (SEQ ID NO: 50) 1 319
Segment cluster Z25377_PEA.sub.--1_node.sub.--12 (SEQ ID NO:198)
according to the present invention is supported by 2 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T8 (SEQ ID NO:45). Table 16 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00320 TABLE 16 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T8 (SEQ ID NO: 45) 304 708
Segment cluster Z25377_PEA.sub.--1_node.sub.--15 (SEQ ID NO:199)
according to the present invention is supported by 19 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T1 (SEQ ID NO:42), Z25377_PEA.sub.--1_T7 (SEQ ID
NO:44), Z25377_PEA.sub.--1_T9 (SEQ ID NO:46),
Z25377_PEA.sub.--1_T11 (SEQ ID NO:48), Z25377_PEA.sub.--1_T12 (SEQ
ID NO:49) and Z25377_PEA.sub.--1_T13 (SEQ ID NO:50). Table 17 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00321 TABLE 17 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T1 (SEQ ID NO: 42) 304 441 Z25377_PEA_1_T7 (SEQ ID NO:
44) 304 441 Z25377_PEA_1_T9 (SEQ ID NO: 46) 304 441
Z25377_PEA_1_T11 (SEQ ID NO: 48) 519 656 Z25377_PEA_1_T12 (SEQ ID
NO: 49) 519 656 Z25377_PEA_1_T13 (SEQ ID NO: 50) 519 656
Segment cluster Z25377_PEA.sub.--1_node.sub.--17 (SEQ ID NO:200)
according to the present invention is supported by 16 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T5 (SEQ ID NO:43). Table 18 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00322 TABLE 18 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T5 (SEQ ID NO: 43) 304 491
Segment cluster Z25377_PEA.sub.--1_node.sub.--18 (SEQ ID NO:201)
according to the present invention is supported by 55 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T5 (SEQ ID NO:43). Table 19 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00323 TABLE 19 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T5 (SEQ ID NO: 43) 492 3969
Segment cluster Z25377_PEA.sub.--1_node.sub.--22 (SEQ ID NO:202)
according to the present invention is supported by 6 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T1 (SEQ ID NO:42), Z25377_PEA.sub.--1_T7 (SEQ ID
NO:44), Z25377_PEA.sub.--1_T10 (SEQ ID NO:47),
Z25377_PEA.sub.--1_T11 (SEQ ID NO:48) and Z25377_PEA.sub.--1_T13
(SEQ ID NO:50). Table 20 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00324 TABLE 20 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T1 (SEQ ID NO: 42) 442 868 Z25377_PEA_1_T7 (SEQ ID NO:
44) 552 978 Z25377_PEA_1_T10 (SEQ ID NO: 47) 304 730
Z25377_PEA_1_T11 (SEQ ID NO: 48) 767 1193 Z25377_PEA_1_T13 (SEQ ID
NO: 50) 657 1083
Segment cluster Z25377_PEA.sub.--1_node.sub.--24 (SEQ ID NO:203)
according to the present invention is supported by 1 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T9 (SEQ ID NO:46) and Z25377_PEA.sub.--1_T12
(SEQ ID NO:49). Table 21 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00325 TABLE 21 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T9 (SEQ ID NO: 46) 442 783 Z25377_PEA_1_T12 (SEQ ID
NO: 49) 657 998
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster Z25377_PEA.sub.--1_node.sub.--0 (SEQ ID NO:204)
according to the present invention is supported by 14 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T1 (SEQ ID NO:42), Z25377_PEA.sub.--1_T5 (SEQ ID
NO:43), Z25377_PEA.sub.--1_T7 (SEQ ID NO:44), Z25377_PEA.sub.--1_T8
(SEQ ID NO:45), Z25377_PEA.sub.--1_T9 (SEQ ID NO:46) and
Z25377_PEA.sub.--1_T10 (SEQ ID NO:47). Table 22 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00326 TABLE 22 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T1 (SEQ ID NO: 42) 1 104 Z25377_PEA_1_T5 (SEQ ID NO:
43) 1 104 Z25377_PEA_1_T7 (SEQ ID NO: 44) 1 104 Z25377_PEA_1_T8
(SEQ ID NO: 45) 1 104 Z25377_PEA_1_T9 (SEQ ID NO: 46) 1 104
Z25377_PEA_1_T10 (SEQ ID NO: 47) 1 104
Segment cluster Z25377_PEA.sub.--1_node.sub.--7 (SEQ ID NO:205)
according to the present invention is supported by 19 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T1 (SEQ ID NO:42), Z25377_PEA.sub.--1_T5 (SEQ ID
NO:43), Z25377_PEA.sub.--1_T7 (SEQ ID NO:44), Z25377_PEA.sub.--1_T8
(SEQ ID NO:45), Z25377_PEA.sub.--1_T9 (SEQ ID NO:46),
Z25377_PEA.sub.--1_T10 (SEQ ID NO:47), Z25377_PEA.sub.--1_T11 (SEQ
ID NO:48), Z25377_PEA.sub.--1_T12 (SEQ ID NO:49) and
Z25377_PEA.sub.--1_T13 (SEQ ID NO:50). Table 23 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00327 TABLE 23 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T1 (SEQ ID NO: 42) 105 199 Z25377_PEA_1_T5 (SEQ ID NO:
43) 105 199 Z25377_PEA_1_T7 (SEQ ID NO: 44) 105 199 Z25377_PEA_1_T8
(SEQ ID NO: 45) 105 199 Z25377_PEA_1_T9 (SEQ ID NO: 46) 105 199
Z25377_PEA_1_T10 (SEQ ID NO: 47) 105 199 Z25377_PEA_1_T11 (SEQ ID
NO: 48) 320 414 Z25377_PEA_1_T12 (SEQ ID NO: 49) 320 414
Z25377_PEA_1_T13 (SEQ ID NO: 50) 320 414
Segment cluster Z25377_PEA.sub.--1_node.sub.--8 (SEQ ID NO:206)
according to the present invention can be found in the following
transcript(s): Z25377_PEA.sub.--1_T1 (SEQ ID NO:42),
Z25377_PEA.sub.--1_T5 (SEQ ID NO:43), Z25377_PEA.sub.--1_T7 (SEQ ID
NO:44), Z25377_PEA.sub.13 1_T8 (SEQ ID NO:45), Z25377_PEA.sub.--_T9
(SEQ ID NO:46), Z25377_PEA.sub.--1_T10 (SEQ ID NO:47),
Z25377_PEA.sub.--1_T11 (SEQ ID NO:48), Z25377_PEA.sub.--1_T12 (SEQ
ID NO:49) and Z25377_PEA.sub.--1_T13 (SEQ ID NO:50). Table 24 below
describes the starting and ending position of this segment on each
transcript.
TABLE-US-00328 TABLE 24 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T1 (SEQ ID NO: 42) 200 204 Z25377_PEA_1_T5 (SEQ ID NO:
43) 200 204 Z25377_PEA_1_T7 (SEQ ID NO: 44) 200 204 Z25377_PEA_1_T8
(SEQ ID NO: 45) 200 204 Z25377_PEA_1_T9 (SEQ ID NO: 46) 200 204
Z25377_PEA_1_T10 (SEQ ID NO: 47) 200 204 Z25377_PEA_1_T11 (SEQ ID
NO: 48) 415 419 Z25377_PEA_1_T12 (SEQ ID NO: 49) 415 419
Z25377_PEA_1_T13 (SEQ ID NO: 50) 415 419
Segment cluster Z25377_PEA.sub.--1_node.sub.--10 (SEQ ID NO:207)
according to the present invention is supported by 20 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T1 (SEQ ID NO:42), Z25377_PEA.sub.--1_T5 (SEQ ID
NO:43), Z25377_PEA.sub.--1_T7 (SEQ ID NO:44), Z25377_PEA.sub.--1_T8
(SEQ ID NO:45), Z25377_PEA.sub.--1_T9 (SEQ ID NO:46),
Z25377_PEA.sub.--1_T10 (SEQ ID NO:47), Z25377_PEA.sub.--1_T11 (SEQ
ID NO:48), Z25377_PEA.sub.--1_T12 (SEQ ID NO:49) and
Z25377_PEA.sub.--1_T13 (SEQ ID NO:50). Table 25 below describes the
starting and ending position of this segment on each
transcript.
TABLE-US-00329 TABLE 25 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T1 (SEQ ID NO: 42) 205 303 Z25377_PEA_1_T5 (SEQ ID NO:
43) 205 303 Z25377_PEA_1_T7 (SEQ ID NO: 44) 205 303 Z25377_PEA_1_T8
(SEQ ID NO: 45) 205 303 Z25377_PEA_1_T9 (SEQ ID NO: 46) 205 303
Z25377_PEA_1_T10 (SEQ ID NO: 47) 205 303 Z25377_PEA_1_T11 (SEQ ID
NO: 48) 420 518 Z25377_PEA_1_T12 (SEQ ID NO: 49) 420 518
Z25377_PEA_1_T13 (SEQ ID NO: 50) 420 518
Segment cluster Z25377_PEA.sub.--1_node.sub.--20 (SEQ ID NO:208)
according to the present invention is supported by 1 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
Z25377_PEA.sub.--1_T7 (SEQ ID NO:44) and Z25377_PEA.sub.--1_T111
(SEQ ID NO:48). Table 26 below describes the starting and ending
position of this segment on each transcript.
TABLE-US-00330 TABLE 26 Segment location on transcripts Segment
starting Segment Transcript name position ending position
Z25377_PEA_1_T7 (SEQ ID NO: 44) 442 551 Z25377_PEA_1_T11 (SEQ ID
NO: 48) 657 766
Variant Protein Alignment to the Previously Known Protein: Sequence
name: BAC85244 (SEQ ID NO:341) Alignment of: Z25377_PEA.sub.--1_P12
(SEQ ID NO:317)+BAC85244 (SEQ ID NO:341)
TABLE-US-00331 Alignment segment 1/1: Quality: 1575.00 Escore: 0
Matching length: 158 Total length: 158 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00047## Sequence name: BAC85244 (SEQ ID NO:341) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P13 (SEQ ID
NO:318)+BAC85244 (SEQ ID NO:341)
TABLE-US-00332 Alignment segment 1/1: Quality: 1558.00 Escore: 0
Matching length: 156 Total length: 156 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00048## Sequence name: BAC85244 (SEQ ID NO:341) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P14 (SEQ ID
NO:319)+BAC85244 (SEQ ID NO:341)
TABLE-US-00333 Alignment segment 1/1: Quality: 1559.00 Escore: 0
Matching length: 162 Total length: 162 Matching Percent 98.15
Matching Percent Identity: 97.53 Similarity: Total Percent
Similarity: 98.15 Total Percent Identity: 97.53 Gaps: 0
Alignment:
##STR00049## Sequence name: Q96NR4 (SEQ ID NO:342) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P15 (SEQ ID
NO:320)+Q96NR4 (SEQ ID NO:342).
TABLE-US-00334 Alignment segment 1/1: Quality: 572.00 Escore: 0
Matching length: 66 Total length: 66 Matching Percent 95.45
Matching Percent Identity: 93.94 Similarity: Total Percent
Similarity: 95.45 Total Percent Identity: 93.94 Gaps: 0
Alignment:
##STR00050## Sequence name: BAC85244 (SEQ ID NO:341) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P15 (SEQ ID
NO:320)+BAC85244 (SEQ ID NO:341)
TABLE-US-00335 Alignment segment 1/1: Quality: 572.00 Escore: 0
Matching length: 66 Total length: 66 Matching Percent 95.45
Matching Percent Identity: 93.94 Similarity: Total Percent
Similarity: 95.45 Total Percent Identity: 93.94 Gaps: 0
Alignment:
##STR00051## Sequence name: Q96NR4 (SEQ ID NO:342) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P17 (SEQ ID
NO:321)+Q96NR4 (SEQ ID NO:342).
TABLE-US-00336 Alignment segment 1/1: Quality: 744.00 Escore: 0
Matching length: 87 Total length: 133 Matching Percent 98.85
Matching Percent Identity: 98.85 Similarity: Total Percent
Similarity: 64.66 Total Percent Identity: 64.66 Gaps: 1
Alignment:
##STR00052## Sequence name: Q8WW45 (SEQ ID NO:343) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P17 (SEQ ID
NO:321)+Q8WW45 (SEQ ID NO:343).
TABLE-US-00337 Alignment segment 1/1: Quality: 711.00 Escore: 0
Matching length: 75 Total length: 75 Matching Percent 97.33
Matching Percent Identity: 97.33 Similarity: Total Percent
Similarity: 97.33 Total Percent Identity: 97.33 Gaps: 0
Alignment:
##STR00053## Sequence name: BAC85244 (SEQ ID NO:341) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P17 (SEQ ID
NO:321)+BAC85244 (SEQ ID NO:341)
TABLE-US-00338 Alignment segment 1/1: Quality: 744.00 Escore: 0
Matching length: 87 Total length: 133 Matching Percent 98.85
Matching Percent Identity: 98.85 Similarity: Total Percent
Similarity: 64.66 Total Percent Identity: 64.66 Gaps: 1
Alignment:
##STR00054## Sequence name: Q96NR4 (SEQ ID NO:342) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P18 (SEQ ID
NO:322)+Q96NR4 (SEQ ID NO:342).
TABLE-US-00339 Alignment segment 1/1: Quality: 588.00 Escore: 0
Matching length: 62 Total length: 62 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00055## Sequence name: Q8WW45 (SEQ ID NO:343) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P18 (SEQ ID
NO:322)+Q8WW45 (SEQ ID NO:343).
TABLE-US-00340 Alignment segment 1/1: Quality: 358.00 Escore: 0
Matching length: 39 Total length: 39 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00056## Sequence name: BAC85244 (SEQ ID NO:341) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P18 (SEQ ID
NO:322)+BAC85244 (SEQ ID NO:341)
TABLE-US-00341 Alignment segment 1/1: Quality: 588.00 Escore: 0
Matching length: 62 Total length: 62 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00057## Sequence name: Q96NR4 (SEQ ID NO:342) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P20 (SEQ ID
NO:324)+Q96NR4 (SEQ ID NO:342).
TABLE-US-00342 Alignment segment 1/1: Quality: 571.00 Escore: 0
Matching length: 60 Total length: 60 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00058## Sequence name: Q8WW45 (SEQ ID NO:343) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P20 (SEQ ID
NO:324)+Q8WW45 (SEQ ID NO:343).
TABLE-US-00343 Alignment segment 1/1: Quality: 341.00 Escore: 0
Matching length: 37 Total length: 37 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00059## Sequence name: BAC85244 (SEQ ID NO:341) Sequence
documentation: Alignment of: Z25377_PEA.sub.--1_P20 (SEQ ID
NO:324)+BAC85244 (SEQ ID NO:341).
TABLE-US-00344 Alignment segment 1/1: Quality: 571.00 Escore: 0
Matching length: 60 Total length: 60 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00060##
Description for Cluster HSACMHCP
Cluster HSACMHCP features 10 transcript(s) and 65 segment(s) of
interest, the names for which are given in Tables 1 and 2,
respectively, the sequences themselves are given at the end of the
application. The selected protein variants are given in table
3.
TABLE-US-00345 TABLE 1 Transcripts of interest Transcript Name SEQ
ID NO: HSACMHCP_PEA_1_T2 51 HSACMHCP_PEA_1_T3 52 HSACMHCP_PEA_1_T4
53 HSACMHCP_PEA_1_T6 54 HSACMHCP_PEA_1_T7 55 HSACMHCP_PEA_1_T8 56
HSACMHCP_PEA_1_T13 57 HSACMHCP_PEA_1_T14 58 HSACMHCP_PEA_1_T17 59
HSACMHCP_PEA_1_T26 60
TABLE-US-00346 TABLE 2 Segments of interest Segment Name Seq ID No.
HSACMHCP_PEA_1_node_2 209 HSACMHCP_PEA_1_node_20 210
HSACMHCP_PEA_1_node_22 211 HSACMHCP_PEA_1_node_25 212
HSACMHCP_PEA_1_node_43 213 HSACMHCP_PEA_1_node_45 214
HSACMHCP_PEA_1_node_46 215 HSACMHCP_PEA_1_node_48 216
HSACMHCP_PEA_1_node_49 217 HSACMHCP_PEA_1_node_57 218
HSACMHCP_PEA_1_node_59 219 HSACMHCP_PEA_1_node_61 220
HSACMHCP_PEA_1_node_63 221 HSACMHCP_PEA_1_node_65 222
HSACMHCP_PEA_1_node_67 223 HSACMHCP_PEA_1_node_71 224
HSACMHCP_PEA_1_node_81 225 HSACMHCP_PEA_1_node_87 226
HSACMHCP_PEA_1_node_89 227 HSACMHCP_PEA_1_node_96 228
HSACMHCP_PEA_1_node_97 229 HSACMHCP_PEA_1_node_100 230
HSACMHCP_PEA_1_node_105 231 HSACMHCP_PEA_1_node_106 232
HSACMHCP_PEA_1_node_107 233 HSACMHCP_PEA_1_node_108 234
HSACMHCP_PEA_1_node_111 235 HSACMHCP_PEA_1_node_113 236
HSACMHCP_PEA_1_node_0 237 HSACMHCP_PEA_1_node_3 238
HSACMHCP_PEA_1_node_4 239 HSACMHCP_PEA_1_node_16 240
HSACMHCP_PEA_1_node_18 241 HSACMHCP_PEA_1_node_23 242
HSACMHCP_PEA_1_node_27 243 HSACMHCP_PEA_1_node_29 244
HSACMHCP_PEA_1_node_31 245 HSACMHCP_PEA_1_node_33 246
HSACMHCP_PEA_1_node_35 247 HSACMHCP_PEA_1_node_37 248
HSACMHCP_PEA_1_node_39 249 HSACMHCP_PEA_1_node_40 250
HSACMHCP_PEA_1_node_51 251 HSACMHCP_PEA_1_node_53 252
HSACMHCP_PEA_1_node_55 253 HSACMHCP_PEA_1_node_69 254
HSACMHCP_PEA_1_node_72 255 HSACMHCP_PEA_1_node_73 256
HSACMHCP_PEA_1_node_74 257 HSACMHCP_PEA_1_node_77 258
HSACMHCP_PEA_1_node_78 259 HSACMHCP_PEA_1_node_80 260
HSACMHCP_PEA_1_node_82 261 HSACMHCP_PEA_1_node_83 262
HSACMHCP_PEA_1_node_84 263 HSACMHCP_PEA_1_node_85 264
HSACMHCP_PEA_1_node_90 265 HSACMHCP_PEA_1_node_91 266
HSACMHCP_PEA_1_node_92 267 HSACMHCP_PEA_1_node_93 268
HSACMHCP_PEA_1_node_95 269 HSACMHCP_PEA_1_node_98 270
HSACMHCP_PEA_1_node_103 271 HSACMHCP_PEA_1_node_104 272
HSACMHCP_PEA_1_node_109 273
TABLE-US-00347 TABLE 3 Proteins of interest Seq ID Protein Name No.
Corresponding Transcript(s) HSACMHCP_PEA_1_P2 326 HSACMHCP_PEA_1_T2
(SEQ ID NO: 51); HSACMHCP_PEA_1_T6 (SEQ ID NO: 54)
HSACMHCP_PEA_1_P3 327 HSACMHCP_PEA_1_T3 (SEQ ID NO: 52)
HSACMHCP_PEA_1_P4 328 HSACMHCP_PEA_1_T4 (SEQ ID NO: 53)
HSACMHCP_PEA_1_P6 329 HSACMHCP_PEA_1_T7 (SEQ ID NO: 55)
HSACMHCP_PEA_1_P12 330 HSACMHCP_PEA_1_T13 (SEQ ID NO: 57)
HSACMHCP_PEA_1_P16 331 HSACMHCP_PEA_1_T17 (SEQ ID NO: 59)
HSACMHCP_PEA_1_P25 332 HSACMHCP_PEA_1_T26 (SEQ ID NO: 60)
HSACMHCP_PEA_1_P28 333 HSACMHCP_PEA_1_T8 (SEQ ID NO: 56)
HSACMHCP_PEA_1_P29 334 HSACMHCP_PEA_1_T14 (SEQ ID NO: 58)
These sequences are variants of the known protein Myosin heavy
chain, cardiac muscle alpha isoform (SEQ ID NO:391) (SwissProt
accession identifier MYH6_HUMAN; known also according to the
synonyms MyHC-alpha), referred to herein as the previously known
protein.
Protein Myosin heavy chain, cardiac muscle alpha isoform (SEQ ID
NO:391) is known or believed to have the following function(s):
Muscle contraction. The sequence for protein Myosin heavy chain,
cardiac muscle alpha isoform is given at the end of the
application, as "Myosin heavy chain, cardiac muscle alpha isoform
amino acid sequence" (SEQ ID NO:391). Known polymorphisms for this
sequence are as shown in Table 4.
TABLE-US-00348 TABLE 4 Amino acid mutations for Known Protein SNP
position(s) on amino acid sequence Comment 88 Q -> E 574 Q ->
P 608 A -> G 744 T -> A 790 M -> I 1014 V -> A 1021 S
-> T 1101 A -> V 1290 A -> S 1373 W -> C.sup. 1533 K
-> N 1540 L -> M 1577-1578 KL -> NV 1705-1706 EQ -> DR
1733 E -> D 1734 A -> S 1737 T -> S 1763 D -> H 1788 M
-> I 1871 D -> N 1882 R -> G 1890 Q -> R 1933
Missing
Protein Myosin heavy chain, cardiac muscle alpha isoform (SEQ ID
NO:391) localization is believed to be Thick filaments of the
myofibrils.
The following GO Annotation(s) apply to the previously known
protein. The following annotation(s) were found: muscle
contraction; striated muscle contraction; muscle development, which
are annotation(s) related to Biological Process; microfilament
motor; actin binding; calmodulin binding; ATP binding, which are
annotation(s) related to Molecular Function; and muscle myosin;
muscle thick filament; myosin, which are annotation(s) related to
Cellular Component.
The GO assignment relies on information from one or more of the
SwissProt/TremB1 Protein knowledgebase, available from <dot
expasy dot ch/sprot/>; or Locuslink, available from <dot ncbi
dot nlm dot nih dot gov/projects/LocusLink/>.
The heart-selective diagnostic marker prediction engine provided
the following results with regard to cluster HSACMHCP. Predictions
were made for selective expression of transcripts of this cluster
in heart tissue, according to the previously described methods. The
numbers on the y-axis of FIG. 30 refer to weighted expression of
ESTs in each category, as "parts per million" (ratio of the
expression of ESTs for a particular cluster to the expression of
all ESTs in that category, according to parts per million).
Overall, the following results were obtained as shown with regard
to the histogram in FIG. 30, concerning the number of
heart-specific clones in libraries/sequences; as well as with
regard to the histogram in FIGS. 31-32, concerning the actual
expression of oligonucleotides in various tissues, including
heart.
This cluster was found to be selectively expressed in heart for the
following reasons: in a comparison of the ratio of expression of
the cluster in heart specific ESTs to the overall expression of the
cluster in non-heart ESTs, which was found to be 24; the ratio of
expression of the cluster in heart specific ESTs to the overall
expression of the cluster in muscle-specific ESTs which was found
to be 92.5; and fisher exact test P-values were computed both for
library and weighted clone counts to check that the counts are
statistically significant, and were found to be 3.20 E-47.
One particularly important measure of specificity of expression of
a cluster in heart tissue is the previously described comparison of
the ratio of expression of the cluster in heart as opposed to
muscle. This cluster was found to be specifically expressed in
heart as opposed to non-heart ESTs as described above. However,
many proteins have been shown to be generally expressed at a higher
level in both heart and muscle, which is less desirable. For this
cluster, as described above, the ratio of expression of the cluster
in heart specific ESTs to the overall expression of the cluster in
muscle-specific ESTs which was found to be 24, which clearly
supports specific expression in heart tissue.
As noted above, cluster HSACMHCP features 10 transcript(s), which
were listed in Table 1 above. These transcript(s) encode for
protein(s) which are variant(s) of protein Myosin heavy chain,
cardiac muscle alpha isoform (SEQ ID NO:391). A description of each
variant protein according to the present invention is now
provided.
Variant protein HSACMHCP_PEA.sub.--1_P2 (SEQ ID NO:326) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51). An alignment is given to
the known protein (Myosin heavy chain, cardiac muscle alpha isoform
(SEQ ID NO:391)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HSACMHCP_PEA.sub.--1_P2 (SEQ ID NO:326)
and MYH6_HUMAN_V1 (SEQ ID NO:338):
1. An isolated chimeric polypeptide encoding for
HSACMHCP_PEA.sub.--1_P2 (SEQ ID NO:326), comprising a first amino
acid sequence being at least 90% homologous to
MTDAQMADFGAAAQYLRKSEKERLEAQTRPFDIRTECFVPDDKEEFVKAKILSREGGK
VIAETENGKTVTVKEDQVLQQNPPKFDKIEDMAMLTFLHEPAVLFNLKERYAAWMIYT
YSGLFCVTVNPYKWLPVYNAEVVAAYRGKKRSEAPPHIFSISDNAYQYMLTDRENQSI
LITGESGAGKTVNTKRVIQYFASIAAIGDRGKKDNANANKGTLEDQIIQANPALEAFGN
AKTVRNDNSSRFGKFIRIHFGATGKLASADIETYLLEKSRVIFQLKAERNYHIFYQILSNK
KPELLDMLLVTNNPYDYAFVSQGEVSVASIDDSEELMATDSAFDVLGFTSEEKAGVYK
LTGAIMHYGNMKFKQKQREEQAEPDGTEDADKSAYLMGLNSADLLKGLCHPRVKVG
NEYVTKGQSVQQVYYSIGALAKAVYEKMFNWMVTRINATLETKQPRQYFIGVLDIAGF
EIFDFNSFEQLCINFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLQACIDLIEK
PMGIMSILEEECMFPKATDMTFKAKLYDNHLGKSNNFQKPRNIKGKQEAHFSLIHYAGT
VDYNILGWLEKNKDPLNETVVALYQKSSLKLMATLFSSYATADTGDSGKSKGGKKKG
SSFQTVSALHRENLNKLMTNLRTTHPHFVRCIIPNERKAPGVMDNPLVMHQLRCNGVL
EGIRICRKGFPNRILYGDFRQRYRILNPVAIPEGQFIDSRKGTEKLLSSLDIDHNQYKFGH
TKVFFKAGLLGLLEEMRDERLSRIITRMQAQARGQLMRIEFKKIVERRDALLVIQWNIR
AFMGVKNWPWMKLYFKIKPLLKSAETEKEMATMKEEFGRIKETLEKSEARRKELEEK
MVSLLQEKNDLQLQVQAEQDNLNDAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMN
AELTAKKRKLEDECSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDEIIAKL
TKEKKALQEAHQQALDDLQVEEDKVNSLSKSKVKLEQQVDDLEGSLEQEKKVRMDLE
RAKRKLEGDLKLTQESIMDLENDKLQLEEKLKKKEFDINQQNSKIEDEQALALQLQKK
LKENQARIEELEEELEAERTARAKVEKLRSDLSRELEEISERLEEAGGATSVQIEMNKKR
EAEFQKMRRDLEEATLQHEATAAALRKKHADSVAELGEQIDNLQRVKQKLEKEKSEF
KLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEEAQRSLNDFTTQRAKLQT
ENGELARQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGKAKNALAHALQSARHDC
DLLREQYEEETEAKAELQRVLSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQ
DAEEAVEAVNAKCSSLEKTKHRLQNEIEDLMVDVERSNAAAAALDKKQRNFDKILAE
WKQKYEESQSELESSQKEARSLSTELFKLKNAYEESLEHLETFKRENKNLQEEISDLTEQ
LGEGGKNVHELEKVRKQLEVEKLELQSALEEAEASLEHEEGKILRAQLEFNQIKAEIER
KLAEKDEEMEQAKRNHQRVVDSLQTSLDAETRSRNEVLRVKKKMEGDLNEMEIQLSH
ANRMAAEAQKQVKSLQSLLKDTQIQLDDAVRANDDLKENIAIVERRNNLLQAELEELR
AVVEQTERSRKLAEQELIETSERVQLLHSQNTSLINQKKKMESDLTQLQSEVEEAVQEC
RNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNMEQTIKDLQHRLDEAEQIAL
KGGKKQLQKLEARVRELEGELEAEQKRNAESVKGMRKSERRIKELTYQ corresponding to
amino acids 1-1855 of MYH6_HUMAN_V1 (SEQ ID NO:338), which also
corresponds to amino acids 1-1855 of HSACMHCP_PEA.sub.--1_P2 (SEQ
ID NO:326), and a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence
VRRTPDTGSRCGSFFSGPTAPPSQGSSHLLLEMLLVDLTFFSRSAVSLT (SEQ ID NO:394)
corresponding to amino acids 1856-1904 of HSACMHCP_PEA.sub.--1_P2
(SEQ ID NO:326), wherein said first amino acid sequence and second
amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
HSACMHCP_PEA.sub.--1_P2 (SEQ ID NO:326), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VRRTPDTGSRCGSFFSGPTAPPSQGSSHLLLEMLLVDLTFFSRSAVSLT (SEQ ID NO:394)
in HSACMHCP_PEA.sub.--1_P2 (SEQ ID NO:326).
It should be noted that the known protein sequence (MYH6_HUMAN; SEQ
ID NO:391) has one or more changes than the sequence given at the
end of the application and named as being the amino acid sequence
for MYH6_HUMAN_V1 (SEQ ID NO:338). These changes were previously
known to occur and are listed in the table below.
TABLE-US-00349 TABLE 5 Changes to MYH6_HUMAN_V1 (SEQ ID NO: 338)
SNP position(s) on amino acid sequence Type of change 89 conflict
1735 conflict
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HSACMHCP_PEA.sub.--1_P2 (SEQ ID NO:326) is encoded
by the following transcript(s): HSACMHCP_PEA.sub.--1_T2 (SEQ ID
NO:51), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51) is shown in bold; this
coding portion starts at position 78 and ends at position 5789. The
transcript also has the following SNPs as listed in Table 6 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein HSACMHCP_PEA.sub.--1_P2 (SEQ ID NO:326) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00350 TABLE 6 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
339 G -> C Yes 488 A -> G Yes 504 A -> C Yes 887 G -> A
Yes 1204 C -> A Yes 1205 A -> C Yes 1232 G -> T No 1696 T
-> G No 2424 C -> A Yes 2910 C -> T Yes 3379 C -> T Yes
3465 G -> A No 4066 C -> No 4088 G -> A Yes 4391 T -> C
Yes 4394 T -> C Yes 4991 C -> T No 5057 C -> T Yes 5279 G
-> T Yes 5282 T -> C Yes 5286 A -> T Yes 5336 C -> T
Yes 5664 G -> A Yes 6141 C -> T Yes 7365 T -> C Yes 7432 G
-> T Yes 7665 A -> G Yes 8268 C -> G Yes 8468 G -> A No
8491 G -> A Yes 8534 C -> T Yes
Variant protein HSACMHCP_PEA.sub.--1_P3 (SEQ ID NO:327) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52). An alignment is given to
the known protein (Myosin heavy chain, cardiac muscle alpha isoform
(SEQ ID NO:391)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HSACMHCP_PEA.sub.--1_P3 (SEQ ID NO:327)
and MYH6_HUMAN_V2 (SEQ ID NO:339):
1. An isolated chimeric polypeptide encoding for
HSACMHCP_PEA.sub.--1_P3 (SEQ ID NO:327), comprising a first amino
acid sequence being at least 90% homologous to
MTDAQMADFGAAAQYLRKSEKERLEAQTRPFDIRTECFVPDDKEEFVKAKILSREGGK
VIAETENGKTVTVKEDQVLQQNPPKFDKIEDMAMLTFLHEPAVLFNLKERYAAWMIYT
YSGLFCVTVNPYKWLPVYNAEVVAAYRGKKRSEAPPHIFSISDNAYQYMLTDRENQSI
LITGESGAGKTVNTKRVIQYFASIAAIGDRGKKDNANANKGTLEDQIIQANPALEAFGN
AKTVRNDNSSRFGKFIRIHFGATGKLASADIETYLLEKSRVIFQLKAERNYHIFYQILSNK
KPELLDMLLVTNNPYDYAFVSQGEVSVASIDDSEELMATDSAFDVLGFTSEEKAGVYK
LTGAIMHYGNMKFKQKQREEQAEPDGTEDADKSAYLMGLNSADLLKGLCHPRVKVG
NEYVTKGQSVQQVYYSIGALAKAVYEKMFNWMVTRINATLETKQPRQYFIGVLDIAGF
EIFDFNSFEQLCINFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLQACIDLIEK
PMGIMSILEEECMFPKATDMTFKAKLYDNHLGKSNNFQKPRNIKGKQEAHFSLIHYAGT
VDYNILGWLEKNKDPLNETVVALYQKSSLKLMATLFSSYATADTGDSGKSKGGKKKG
SSFQTVSALHRENLNKLMTNLRTTHPHFVRCIIPNERKAPGVMDNPLVMHQLRCNGVL
EGIRICRKGFPNRILYGDFRQRYRILNPVAIPEGQFIDSRKGTEKLLSSLDIDHNQYKFGH
TKVFFKAGLLGLLEEMRDERLSRIITRMQAQARGQLMRIEFKKIVERRDALLVIQWNIR
AFMGVKNWPWMKLYFKIKPLLKSAETEKEMATMKEEFGRIKETLEKSEARRKELEEK
MVSLLQEKNDLQLQVQAEQDNLNDAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMN
AELTAKKRKLEDECSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDEIIAKL
TKEKKALQEAHQQALDDLQVEEDKVNSLSKSKVKLEQQVDDLEGSLEQEKKVRMDLE
RAKRKLEGDLKLTQESIMDLENDKLQLEEKLKKKEFDINQQNSKIEDEQALALQLQKK
LKENQARIEELEEELEAERTARAKVEKLRSDLSRELEEISERLEEAGGATSVQIEMNKKR
EAEFQKMRRDLEEATLQHEATAAALRKKHADSVAELGEQIDNLQRVKQKLEKEKSEF
KLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEEAQRSLNDFTTQRAKLQT
ENGELARQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGK corresponding to amino
acids 1-1326 of MYH6_HUMAN_V2 (SEQ ID NO:339), which also
corresponds to amino acids 1-1326 of HSACMHCP_PEA.sub.--1_P3 (SEQ
ID NO:327), and a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence VRPSGEGGQA (SEQ ID NO:431)
corresponding to amino acids 1327-1336 of HSACMHCP_PEA.sub.--1_P3
(SEQ ID NO:327), wherein said first amino acid sequence and second
amino acid sequence are contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
HSACMHCP_PEA.sub.--1_P3 (SEQ ID NO:327), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence VRPSGEGGQA
(SEQ ID NO:431) in HSACMHCP_PEA.sub.--1_P3 (SEQ ID NO:327).
It should be noted that the known protein sequence (MYH6_HUMAN (SEQ
ID NO:391)) has one or more changes than the sequence given at the
end of the application and named as being the amino acid sequence
for MYH6_HUMAN_V2 (SEQ ID NO:339). These changes were previously
known to occur and are listed in the table below.
TABLE-US-00351 TABLE 7 Changes to MYH6_HUMAN_V2 (SEQ ID NO: 339)
SNP position(s) on amino acid sequence Type of change 89
conflict
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HSACMHCP_PEA.sub.--1_P3 (SEQ ID NO:327) also has
the following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 8, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein HSACMHCP_PEA.sub.--1_P3 (SEQ ID
NO:327) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00352 TABLE 8 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
88 E -> Q Yes 376 P -> Q Yes 540 M -> R No 783 L -> M
Yes 1101 A -> V Yes 1130 A -> T No
Variant protein HSACMHCP_PEA.sub.--1_P3 (SEQ ID NO:327) is encoded
by the following transcript(s): HSACMHCP_PEA.sub.--1_T3 (SEQ ID
NO:52), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52) is shown in bold; this
coding portion starts at position 78 and ends at position 4085. The
transcript also has the following SNPs as listed in Table 9 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein HSACMHCP_PEA.sub.--1_P3 (SEQ ID NO:327) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00353 TABLE 9 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
339 G -> C Yes 488 A -> G Yes 504 A -> C Yes 887 G -> A
Yes 1204 C -> A Yes 1205 A -> C Yes 1232 G -> T No 1696 T
-> G No 2424 C -> A Yes 2910 C -> T Yes 3379 C -> T Yes
3465 G -> A No 4403 C -> No 4425 G -> A Yes 4728 T -> C
Yes 4731 T -> C Yes 5328 C -> T No 5394 C -> T Yes 5616 G
-> T Yes 5619 T -> C Yes 5623 A -> T Yes 5673 C -> T
Yes
Variant protein HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53). An alignment is given to
the known protein (Myosin heavy chain, cardiac muscle alpha isoform
(SEQ ID NO:391)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328)
and MYH6_HUMAN_V2 (SEQ ID NO:339):
1. An isolated chimeric polypeptide encoding for
HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328), comprising a first amino
acid sequence being at least 90% homologous to
MTDAQMADFGAAAQYLRKSEKERLEAQTRPFDIRTECFVPDDKEEFVKAKILSREGGK
VIAETENGKTVTVKEDQVLQQNPPKFDKIEDMAMLTFLHEPAVLFNLKERYAAWMIYT
YSGLFCVTVNPYKWLPVYNAEVVAAYRGKKRSEAPPHIFSISDNAYQYMLTDRENQSI
LITGESGAGKTVNTKRVIQYFASIAAIGDRGKKDNANANKGTLEDQIIQANPALEAFGN
AKTVRNDNSSRFGKFIRIHFGATGKLASADIETYLLEKSRVIFQLKAERNYHIFYQILSNK
KPELLDMLLVTNNPYDYAFVSQGEVSVASIDDSEELMATDSAFDVLGFTSEEKAGVYK
LTGAIMHYGNMKFKQKQREEQAEPDGTEDADKSAYLMGLNSADLLKGLCHPRVKVG
NEYVTKGQSVQQVYYSIGALAKAVYEKMFNWMVTRINATLETKQPRQYFIGVLDIAGF
EIFDFNSFEQLCINFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLQACIDLIEK
PMGIMSILEEECMFPKATDMTFKAKLYDNHLGKSNNFQKPRNIKGKQEAHFSLIHYAGT
VDYNILGWLEKNKDPLNETVVALYQKSSLKLMATLFSSYATADTGDSGKSKGGKKKG
SSFQTVSALHRENLNKLMTNLRTTHPHFVRCIIPNERKAPGVMDNPLVMHQLRCNGVL
EGIRICRKGFPNRILYGDFRQRYRILNPVAIPEGQFIDSRKGTEKLLSSLDIDHNQYKFGH
TKVFFKAGLLGLLEEMRDERLSRIITRMQAQARGQLMRIEFKKIVERRDALLVIQWNIR
AFMGVKNWPWMKLYFKIKPLLKSAETEKEMATMKEEFGRIKETLEKSEARRKELEEK
MVSLLQEKNDLQLQVQAEQDNLNDAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMN
AELTAKKRKLEDECSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDEIIAKL
TKEKKALQEAHQQALDDLQVEEDKVNSLSKSKVKLEQQVDDLEGSLEQEKKVRMDLE
RAKRKLEGDLKLTQESIMDLENDKLQLEEKLKKKEFDINQQNSKIEDEQALALQLQKK
LKENQARIEELEEELEAERTARAKVEKLRSDLSRELEEISERLEEAGGATSVQIEMNKKR
EAEFQKMRRDLEEATLQHEATAAALRKKHADSVAELGEQIDNLQRVKQKLEKEKSEF
KLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEEAQRSLNDFTTQRAKLQT
ENGELARQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGKAKNALAHALQSARHDC
DLLREQYEEETEAKAELQRVLSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQ
DAEEAVEAVNAKCSSLEKTKHRLQNEIEDLMVDVERSNAAAAALDKKQRNFDKILAE
WKQKYEESQSELESSQKEARSLSTELFKLKNAYEESLEHLETFKRENKNLQ corresponding
to amino acids 1-1508 of MYH6_HUMAN_V2 (SEQ ID NO:339), which also
corresponds to amino acids 1-1508 of HSACMHCP_PEA.sub.--1_P4 (SEQ
ID NO:328), and a second amino acid sequence being at least 70%,
optionally at least 80%, preferably at least 85%, more preferably
at least 90% and most preferably at least 95% homologous to a
polypeptide having the sequence GVLGVQEARDELVGGRAMQGQGEHRL (SEQ ID
NO:432) corresponding to amino acids 1509-1534 of
HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328), wherein said first amino
acid sequence and second amino acid sequence are contiguous and in
a sequential order.
2. An isolated polypeptide encoding for a tail of
HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
GVLGVQEARDELVGGRAMQGQGEHRL (SEQ ID NO:432) in
HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328) also has
the following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 11, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein HSACMHCP_PEA.sub.--1_P4 (SEQ ID
NO:328) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00354 TABLE 11 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
88 E -> Q Yes 376 P -> Q Yes 540 M -> R.sup. No 783 L
-> M Yes 1101 A -> V Yes 1130 A -> T No 1330 A -> .sup.
No
Variant protein HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328) is encoded
by the following transcript(s): HSACMHCP_PEA.sub.--1_T4 (SEQ ID
NO:53), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53) is shown in bold; this
coding portion starts at position 78 and ends at position 4679. The
transcript also has the following SNPs as listed in Table 12 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00355 TABLE 12 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
339 G -> C Yes 488 A -> G Yes 504 A -> C Yes 887 G -> A
Yes 1204 C -> A Yes 1205 A -> C Yes 1232 G -> T No 1696 T
-> G No 2424 C -> A Yes 2910 C -> T Yes 3379 C -> T Yes
3465 G -> A No 4066 C -> No 4088 G -> A Yes 4391 T -> C
Yes 4394 T -> C Yes 4673 T -> C Yes 5095 C -> T No 5161 C
-> T Yes 5383 G -> T Yes 5386 T -> C Yes 5390 A -> T
Yes 5440 C -> T Yes
Variant protein HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55). An alignment is given to
the known protein (Myosin heavy chain, cardiac muscle alpha isoform
(SEQ ID NO:391)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329)
and MYH6_HUMAN_V1 (SEQ ID NO:338):
1. An isolated chimeric polypeptide encoding for
HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329), comprising a first amino
acid sequence being at least 90% homologous to
MTDAQMADFGAAAQYLRKSEKERLEAQTRPFDIRTECFVPDDKEEFVKAKILSREGGK
VIAETENGKTVTVKEDQVLQQNPPKFDKIEDMAMLTFLHEPAVLFNLKERYAAWMIYT
YSGLFCVTVNPYKWLPVYNAEVVAAYRGKKRSEAPPHIFSISDNAYQYMLTDRENQSI
LITGESGAGKTVNTKRVIQYFASIAAIGDRGKKDNANANKGTLEDQIIQANPALEAFGN
AKTVRNDNSSRFGKFIRIHFGATGKLASADIETYLLEKSRVIFQLKAERNYHIFYQILSNK
KPELLDMLLVTNNPYDYAFVSQGEVSVASIDDSEELMATDSAFDVLGFTSEEKAGVYK
LTGAIMHYGNMKFKQKQREEQAEPDGTEDADKSAYLMGLNSADLLKGLCHPRVKVG
NEYVTKGQSVQQVYYSIGALAKAVYEKMFNWMVTRINATLETKQPRQYFIGVLDIAGF
EIFDFNSFEQLCINFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLQACIDLIEK
PMGIMSILEEECMFPKATDMTFKAKLYDNHLGKSNNFQKPRNIKGKQEAHFSLIHYAGT
VDYNILGWLEKNKDPLNETVVALYQKSSLKLMATLFSSYATADTGDSGKSKGGKKKG
SSFQTVSALHRENLNKLMTNLRTTHPHFVRCIIPNERKAPGVMDNPLVMHQLRCNGVL
EGIRICRKGFPNRILYGDFRQRYRILNPVAIPEGQFIDSRKGTEKLLSSLDIDHNQYKFGH
TKVFFKAGLLGLLEEMRDERLSRIITRMQAQARGQLMRIEFKKIVERRDALLVIQWNIR
AFMGVKNWPWMKLYFKIKPLLKSAETEKEMATMKEEFGRIKETLEKSEARRKELEEK
MVSLLQEKNDLQLQVQAEQDNLNDAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMN
AELTAKKRKLEDECSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDEIIAKL
TKEKKALQEAHQQALDDLQVEEDKVNSLSKSKVKLEQQVDDLEGSLEQEKKVRMDLE
RAKRKLEGDLKLTQESIMDLENDKLQLEEKLKKKEFDINQQNSKIEDEQALALQLQKK
LKENQARIEELEEELEAERTARAKVEKLRSDLSRELEEISERLEEAGGATSVQIEMNKKR
EAEFQKMRRDLEEATLQHEATAAALRKKHADSVAELGEQIDNLQRVKQKLEKEKSEF
KLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEEAQRSLNDFTTQRAKLQT
ENGELARQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGKAKNALAHALQSARHDC
DLLREQYEEETEAKAELQRVLSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQ
DAEEAVEAVNAKCSSLEKTKHRLQNEIEDLMVDVERSNAAAAALDKKQRNFDKILAE
WKQKYEESQSELESSQKEARSLSTELFKLKNAYEESLEHLETFKRENKNLQEEISDLTEQ
LGEGGKNVHELEKVRKQLEVEKLELQSALEEAEASLEHEEGKILRAQLEFNQIKAEIER
KLAEKDEEMEQAKRNHQRVVDSLQTSLDAETRSRNEVLRVKKKMEGDLNEMEIQLSH
ANRMAAEAQKQVKSLQSLLKDTQIQLDDAVRANDDLKENIAIVERRNNLLQAELEELR
AVVEQTERSRKLAEQELIETSERVQLLHSQNTSLINQKKKMESDLTQLQSEVEEAVQEC
RNAEEKAKKAITD corresponding to amino acids 1-1763 of MYH6_HUMAN_V 1
(SEQ ID NO:338), which also corresponds to amino acids 1-1763 of
HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
VSDRPPSASPKDRNKALGPGQATVL (SEQ ID NO:432) corresponding to amino
acids 1764-1788 of HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329), wherein
said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VSDRPPSASPKDRNKALGPGQATVL (SEQ ID NO:432) in
HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329) also has
the following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 14, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein HSACMHCP_PEA.sub.--1_P6 (SEQ ID
NO:329) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00356 TABLE 14 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
88 E -> Q Yes 376 P -> Q Yes 540 M -> R.sup. No 783 L
-> M Yes 1101 A -> V Yes 1130 A -> T No 1330 A -> .sup.
No 1737 T -> S Yes
Variant protein HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329) is encoded
by the following transcript(s): HSACMHCP_PEA.sub.--1_T7 (SEQ ID
NO:55), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55) is shown in bold; this
coding portion starts at position 78 and ends at position 5441. The
transcript also has the following SNPs as listed in Table 15 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00357 TABLE 15 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
339 G -> C Yes 488 A -> G Yes 504 A -> C Yes 887 G -> A
Yes 1204 C -> A Yes 1205 A -> C Yes 1232 G -> T No 1696 T
-> G No 2424 C -> A Yes 2910 C -> T Yes 3379 C -> T Yes
3465 G -> A No 4066 C -> No 4088 G -> A Yes 4391 T -> C
Yes 4394 T -> C Yes 4991 C -> T No 5057 C -> T Yes 5279 G
-> T Yes 5282 T -> C Yes 5286 A -> T Yes 5336 C -> T
Yes 5862 G -> A Yes 6339 C -> T Yes 7563 T -> C Yes 7630 G
-> T Yes 7863 A -> G Yes 8466 C -> G Yes 8666 G -> A No
8689 G -> A Yes 8732 C -> T Yes
Variant protein HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57). An alignment is given to
the known protein (Myosin heavy chain, cardiac muscle alpha isoform
(SEQ ID NO:391)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330)
and MYH6_HUMAN_V3 (SEQ ID NO:340):
1. An isolated chimeric polypeptide encoding for
HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330), comprising a first amino
acid sequence being at least 70%, optionally at least 80%,
preferably at least 85%, more preferably at least 90% and most
preferably at least 95% homologous to a polypeptide having the
sequence MGLWKPGSVLSDSLFASSPCPQ (SEQ ID NO:395) corresponding to
amino acids 1-22 of HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330), and a
second amino acid sequence being at least 90% homologous to
PMGIMSILEEECMFPKATDMTFKAKLYDNHLGKSNNFQKPRNIKGKQEAHFSLIHYAGT
VDYNILGWLEKNKDPLNETVVALYQKSSLKLMATLFSSYATADTGDSGKSKGGKKKG
SSFQTVSALHRENLNKLMTNLRTTHPHFVRCIIPNERKAPGVMDNPLVMHQLRCNGVL
EGIRICRKGFPNRILYGDFRQRYRILNPVAIPEGQFIDSRKGTEKLLSSLDIDHNQYKFGH
TKVFFKAGLLGLLEEMRDERLSRIITRMQAQARGQLMRIEFKKIVERRDALLVIQWNIR
AFMGVKNWPWMKLYFKIKPLLKSAETEKEMATMKEEFGRIKETLEKSEARRKELEEK
MVSLLQEKNDLQLQVQAEQDNLNDAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMN
AELTAKKRKLEDECSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDEIIAKL
TKEKKALQEAHQQALDDLQVEEDKVNSLSKSKVKLEQQVDDLEGSLEQEKKVRMDLE
RAKRKLEGDLKLTQESIMDLENDKLQLEEKLKKKEFDINQQNSKIEDEQALALQLQKK
LKENQARIEELEEELEAERTARAKVEKLRSDLSRELEEISERLEEAGGATSVQIEMNKKR
EAEFQKMRRDLEEATLQHEATAAALRKKHADSVAELGEQIDNLQRVKQKLEKEKSEF
KLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEEAQRSLNDFTTQRAKLQT
ENGELARQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGKAKNALAHALQSARHDC
DLLREQYEEETEAKAELQRVLSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQ
DAEEAVEAVNAKCSSLEKTKHRLQNEIEDLMVDVERSNAAAAALDKKQRNFDKILAE
WKQKYEESQSELESSQKEARSLSTELFKLKNAYEESLEHLETFKRENKNLQEEISDLTEQ
LGEGGKNVHELEKVRKQLEVEKLELQSALEEAEASLEHEEGKILRAQLEFNQIKAEIER
KLAEKDEEMEQAKRNHQRVVDSLQTSLDAETRSRNEVLRVKKKMEGDLNEMEIQLSH
ANRMAAEAQKQVKSLQSLLKDTQIQLDDAVRANDDLKENIAIVERRNNLLQAELEELR
AVVEQTERSRKLAEQELIETSERVQLLHSQNTSLINQKKKMESDLTQLQSEVEEAVQEC
RNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNMEQTIKDLQHRLDEAEQIAL
KGGKKQLQKLEARVRELEGELEAEQKRNAESVKGMRKSERRIKELTYQTEEDKKNLLR
LQDLVDKLQLKVKAYKRQAEEAEEQANTNLSKFRKVQHELDEAEERADIAESQVNKL
RAKSRDIGAKQKMHDEE corresponding to amino acids 528-1939 of
MYH6_HUMAN_V3 (SEQ ID NO:340), which also corresponds to amino
acids 23-1434 of HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330), wherein
said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
2. An isolated polypeptide encoding for a head of
HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
MGLWKPGSVLSDSLFASSPCPQ (SEQ ID NO:395) of HSACMHCP_PEA.sub.--1_P2
(SEQ ID NO:330).
It should be noted that the known protein sequence (MYH6_HUMAN (SEQ
ID NO:391)) has one or more changes than the sequence given at the
end of the application and named as being the amino acid sequence
for MYH6_HUMAN_V3 (SEQ ID NO:340). These changes were previously
known to occur and are listed in the table below.
TABLE-US-00358 TABLE 16 Changes to MYH6_HUMAN_V3 (SEQ ID NO: 340)
SNP position(s) on amino acid sequence Type of change 1735
conflict
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330) also has
the following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 17, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein HSACMHCP_PEA.sub.--1_P12 (SEQ ID
NO:330) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00359 TABLE 17 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
10 L -> F Yes 35 M -> R.sup. No 278 L -> M Yes 596 A ->
V Yes 625 A -> T No 825 A -> .sup. No 1232 T -> S Yes
Variant protein HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330) is encoded
by the following transcript(s): HSACMHCP_PEA.sub.--1_T13 (SEQ ID
NO:57), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) is shown in bold; this
coding portion starts at position 67 and ends at position 4368. The
transcript also has the following SNPs as listed in Table 18 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00360 TABLE 18 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
94 C -> T Yes 170 T -> G No 898 C -> A Yes 1384 C -> T
Yes 1853 C -> T Yes 1939 G -> A No 2540 C -> No 2562 G
-> A Yes 2865 T -> C Yes 2868 T -> C Yes 3465 C -> T No
3531 C -> T Yes 3753 G -> T Yes 3756 T -> C Yes 3760 A
-> T Yes 3810 C -> T Yes
Variant protein HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59). An alignment is given to
the known protein (Myosin heavy chain, cardiac muscle alpha isoform
(SEQ ID NO:391)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331)
and MYH6_HUMAN_V2 (SEQ ID NO:339):
1. An isolated chimeric polypeptide encoding for
HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331), comprising a first amino
acid sequence being at least 90% homologous to
MTDAQMADFGAAAQYLRKSEKERLEAQTRPFDIRTECFVPDDKEEFVKAKILSREGGK
VIAETENGKTVTVKEDQVLQQNPPKFDKIEDMAMLTFLHEPAVLFNLKERYAAWMIYT
YSGLFCVTVNPYKWLPVYNAEVVAAYRGKKRSEAPPHIFSISDNAYQYMLTDRENQSI
LITGESGAGKTVNTKRVIQYFASIAAIGDRGKKDNANANKGTLEDQIIQANPALEAFGN
AKTVRNDNSSRFGKFIRIHFGATGKLASADIETYLLEKSRVIFQLKAERNYHIFYQILSNK
KPELLDMLLVTNNPYDYAFVSQGEVSVASIDDSEELMATDSAFDVLGFTSEEKAGVYK
LTGAIMHYGNMKFKQKQREEQAEPDGTEDADKSAYLMGLNSADLLKGLCHPRVKVG
NEYVTKGQSVQQVYYSIGALAKAVYEKMFNWMVTRINATLETKQPRQYFIGVLDIAGF
EIFDFNSFEQLCINFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLQACIDLIEK
corresponding to amino acids 1-527 of MYH6_HUMAN_V2 (SEQ ID
NO:339), which also corresponds to amino acids 1-527 of
HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331), and a second amino acid
sequence being at least 70%, optionally at least 80%, preferably at
least 85%, more preferably at least 90% and most preferably at
least 95% homologous to a polypeptide having the sequence
VPPWPHHLCPLLCHPDKVVAESLLHPRN (SEQ ID NO:435) corresponding to amino
acids 528-555 of HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331), wherein
said first amino acid sequence and second amino acid sequence are
contiguous and in a sequential order.
2. An isolated polypeptide encoding for a tail of
HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VPPWPHHLCPLLCHPDKVVAESLLHPRN (SEQ ID NO:435) in
HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331) also has
the following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 20, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein HSACMHCP_PEA.sub.--1_P16 (SEQ ID
NO:331) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00361 TABLE 20 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
88 E -> Q Yes 376 P -> Q Yes
Variant protein HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331) is encoded
by the following transcript(s): HSACMHCP_PEA.sub.--1_T17 (SEQ ID
NO:59), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) is shown in bold; this
coding portion starts at position 78 and ends at position 1742. The
transcript also has the following SNPs as listed in Table 21 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00362 TABLE 21 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
339 G -> C Yes 488 A -> G Yes 504 A -> C Yes 887 G -> A
Yes 1204 C -> A Yes 1205 A -> C Yes 1232 G -> T No 2094 C
-> T Yes 2095 G -> A Yes 2347 A -> G Yes
Variant protein HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). An alignment is given to
the known protein (Myosin heavy chain, cardiac muscle alpha isoform
(SEQ ID NO:391)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332)
and MYH6_HUMAN_V I (SEQ ID NO:338):
1. An isolated chimeric polypeptide encoding for
HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332), comprising a first amino
acid sequence being at least 90% homologous to
MTDAQMADFGAAAQYLRKSEKERLEAQTRPFDIRTECFVPDDKEEFVKAKILSREGGK
VIAETENGKTVTVKEDQVLQQNPPKFDKIEDMAMLTFLHEPAVLFNLKERYAAWMIYT
YSGLFCVTVNPYKWLPVYNAEVVAAYRGKKRSEAPPHIFSISDNAYQYMLTDRENQSI
LITGESGAGKTVNTKRVIQYFASIAAIGDRGKKDNANANKGTLEDQIIQANPALEAFGN
AKTVRNDNSSRFGKFIRIHFGATGKLASADIETYLLEKSRVIFQLKAERNYHIFYQILSNK
KPELLDMLLVTNNPYDYAFVSQGEVSVASIDDSEELMATDSAFDVLGFTSEEKAGVYK
LTGAIMHYGNMKFKQKQREEQAEPDGTEDADKSAYLMGLNSADLLKGLCHPRVKVG
NEYVTKGQSVQQVYYSIGALAKAVYEKMFNWMVTRINATLETKQPRQYFIGVLDIAGF EIFD
corresponding to amino acids 1-470 of MYH6_HUMAN_V1 (SEQ ID
NO:338), which also corresponds to amino acids 1-470 of
HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332), a second amino acid
sequence being at least 90% homologous to
PMGIMSILEEECMFPKATDMTFKAKLYDNHLGKSNNFQKPRNIKGKQEAHFSLIHYAGT
VDYNILGWLEKNKDPLNETVVALYQKSSLKLMATLFSSYATADTGDSGKSKGGKKKG
SSFQTVSALHRENLNKLMTNLRTTHPHFVRCIIPNERKAPGVMDNPLVMHQLRCNGVL
EGIRICRKGFPNRILYGDFRQRYRILNPVAIPEGQFIDSRKGTEKLLSSLDIDHNQYKFGH
TKVFFKAGLLGLLEEMRDERLSRIITRMQAQARGQLMRIEFKKIVERRDALLVIQWNIR
AFMGVKNWPWMKLYFKIKPLLKSAETEKEMATMKEEFGRIKETLEKSEARRKELEEK
MVSLLQEKNDLQLQVQAEQDNLNDAEERCDQLIKNKIQLEAKVKEMNERLEDEEEMN
AELTAKKRKLEDECSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDEIIAKL
TKEKKALQEAHQQALDDLQVEEDKVNSLSKSKVKLEQQVDDLEGSLEQEKKVRMDLE
RAKRKLEGDLKLTQESIMDLENDKLQLEEKLKKKEFDINQQNSKIEDEQALALQLQKK
LKENQARIEELEEELEAERTARAKVEKLRSDLSRELEEISERLEEAGGATSVQIEMNKKR
EAEFQKMRRDLEEATLQHEATAAALRKKHADSVAELGEQIDNLQRVKQKLEKEKSEF
KLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEEAQRSLNDFTTQRAKLQT
ENGELARQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGKAKNALAHALQSARHDC
DLLREQYEEETEAKAELQRVLSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQ
DAEEAVEAVNAKCSSLEKTKHRLQNEIEDLMVDVERSNAAAAALDKKQRNFDKILAE
WKQKYEESQSELESSQKEARSLSTELFKLKNAYEESLEHLETFKRENKNLQEEISDLTEQ
LGEGGKNVHELEKVRKQLEVEKLELQSALEEAEASLEHEEGKILRAQLEFNQIKAEIER
KLAEKDEEMEQAKRNHQRVVDSLQTSLDAETRSRNEVLRVKKKMEGDLNEMEIQLSH
ANRMAAEAQKQVKSLQSLLKDTQIQLDDAVRANDDLKENIAIVERRNNLLQAELEELR
AVVEQTERSRKLAEQELIETSERVQLLHSQNTSLINQKKKMESDLTQLQSEVEEAVQEC
RNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNMEQTIKDLQHRLDEAEQIAL
KGGKKQLQKLEARVRELEGELEAEQKRNAESVKGMRKSERRIKELTYQ corresponding to
amino acids 528-1855 of MYH6_HUMAN_V1 (SEQ ID NO:338), which also
corresponds to amino acids 471-1798 of HSACMHCP_PEA.sub.--1_P25
(SEQ ID NO:332), and a third amino acid sequence being at least
70%, optionally at least 80%, preferably at least 85%, more
preferably at least 90% and most preferably at least 95% homologous
to a polypeptide having the sequence
VRRTPDTGSRCGSFFSGPTAPPSQGSSHLLLEMLLVDLTFFSRSAVSLT (SEQ ID NO:394)
corresponding to amino acids 1799-1847 of HSACMHCP_PEA.sub.--1_P25
(SEQ ID NO:332), wherein said first amino acid sequence, second
amino acid sequence and third amino acid sequence are contiguous
and in a sequential order.
2. An isolated chimeric polypeptide encoding for an edge portion of
HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332), comprising a polypeptide
having a length "n", wherein n is at least about 10 amino acids in
length, optionally at least about 20 amino acids in length,
preferably at least about 30 amino acids in length, more preferably
at least about 40 amino acids in length and most preferably at
least about 50 amino acids in length, wherein at least two amino
acids comprise DP, having a structure as follows: a sequence
starting from any of amino acid numbers 470-x to 470; and ending at
any of amino acid numbers 471+((n-2)-x), in which x varies from 0
to n-2.
3. An isolated polypeptide encoding for a tail of
HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332), comprising a polypeptide
being at least 70%, optionally at least about 80%, preferably at
least about 85%, more preferably at least about 90% and most
preferably at least about 95% homologous to the sequence
VRRTPDTGSRCGSFFSGPTAPPSQGSSHLLLEMLLVDLTFFSRSAVSLT (SEQ ID NO:394)
in HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332) also has
the following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 23, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein HSACMHCP_PEA.sub.--1_P25 (SEQ ID
NO:332) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00363 TABLE 23 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
88 E -> Q Yes 376 P -> Q Yes 483 M -> R.sup. No 726 L
-> M Yes 1044 A -> V Yes 1073 A -> T No 1273 A -> .sup.
No 1680 T -> S Yes 1806 G -> R Yes
Variant protein HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332) is encoded
by the following transcript(s): HSACMHCP_PEA.sub.--1_T26 (SEQ ID
NO:60), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60) is shown in bold; this
coding portion starts at position 78 and ends at position 5618. The
transcript also has the following SNPs as listed in Table 24 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein HSACMHCP_PEA.sub.--1_P25 (SEQ ID NO:332) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00364 TABLE 24 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
339 G -> C Yes 488 A -> G Yes 504 A -> C Yes 887 G -> A
Yes 1204 C -> A Yes 1205 A -> C Yes 1232 G -> T No 1525 T
-> G No 2253 C -> A Yes 2739 C -> T Yes 3208 C -> T Yes
3294 G -> A No 3895 C -> No 3917 G -> A Yes 4220 T -> C
Yes 4223 T -> C Yes 4820 C -> T No 4886 C -> T Yes 5108 G
-> T Yes 5111 T -> C Yes 5115 A -> T Yes 5165 C -> T
Yes 5493 G -> A Yes 5970 C -> T Yes
Variant protein HSACMHCP_PEA.sub.--1_P28 (SEQ ID NO:333) according
to the present on has an amino acid sequence as given at the end of
the application; it is encoded by transcript(s)
HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56). An alignment is given to
the known protein (Myosin heavy chain, cardiac muscle alpha isoform
(SEQ ID NO:391)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HSACMHCP_PEA.sub.--1_P28 (SEQ ID NO:333)
and MYH6_HUMAN_V3 (SEQ ID NO:340):
1. An isolated chimeric polypeptide encoding for
HSACMHCP_PEA.sub.--1_P28 (SEQ ID NO:333), comprising a first amino
acid sequence being at least 90% homologous to
MLTDRENQSILITGESGAGKTVNTKRVIQYFASIAAIGDRGKKDNANANKGTLEDQIIQA
NPALEAFGNAKTVRNDNSSRFGKFIRIHFGATGKLASADIETYLLEKSRVIFQLKAERNY
HIFYQILSNKKPELLDMLLVTNNPYDYAFVSQGEVSVASIDDSEELMATDSAFDVLGFT
SEEKAGVYKLTGAIMHYGNMKFKQKQREEQAEPDGTEDADKSAYLMGLNSADLLKG
LCHPRVKVGNEYVTKGQSVQQVYYSIGALAKAVYEKMFNWMVTRINATLETKQPRQ
YFIGVLDIAGFEIFDFNSFEQLCINFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGM
DLQACIDLIEKPMGIMSILEEECMFPKATDMTFKAKLYDNHLGKSNNFQKPRNIKGKQE
AHFSLIHYAGTVDYNILGWLEKNKDPLNETVVALYQKSSLKLMATLFSSYATADTGDS
GKSKGGKKKGSSFQTVSALHRENLNKLMTNLRTTHPHFVRCIIPNERKAPGVMDNPLV
MHQLRCNGVLEGIRICRKGFPNRILYGDFRQRYRILNPVAIPEGQFIDSRKGTEKLLSSLD
IDHNQYKFGHTKVFFKAGLLGLLEEMRDERLSRIITRMQAQARGQLMRIEFKKIVERRD
ALLVIQWNIRAFMGVKNWPWMKLYFKIKPLLKSAETEKEMATMKEEFGRIKETLEKSE
ARRKELEEKMVSLLQEKNDLQLQVQAEQDNLNDAEERCDQLIKNKIQLEAKVKEMNE
RLEDEEEMNAELTAKKRKLEDECSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEM
AGLDEIIAKLTKEKKALQEAHQQALDDLQVEEDKVNSLSKSKVKLEQQVDDLEGSLEQ
EKKVRMDLERAKRKLEGDLKLTQESIMDLENDKLQLEEKLKKKEFDINQQNSKIEDEQ
ALALQLQKKLKENQARIEELEEELEAERTARAKVEKLRSDLSRELEEISERLEEAGGATS
VQIEMNKKREAEFQKMRRDLEEATLQHEATAAALRKKHADSVAELGEQIDNLQRVKQ
KLEKEKSEFKLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEEAQRSLNDFT
TQRAKLQTENGELARQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGKAKNALAHA
LQSARHDCDLLREQYEEETEAKAELQRVLSKANSEVAQWRTKYETDAIQRTEELEEAK
KKLAQRLQDAEEAVEAVNAKCSSLEKTKHRLQNEIEDLMVDVERSNAAAAALDKKQR
NFDKILAEWKQKYEESQSELESSQKEARSLSTELFKLKNAYEESLEHLETFKRENKNLQ
EEISDLTEQLGEGGKNVHELEKVRKQLEVEKLELQSALEEAEASLEHEEGKILRAQLEF
NQIKAEIERKLAEKDEEMEQAKRNHQRVVDSLQTSLDAETRSRNEVLRVKKKMEGDL
NEMEIQLSHANRMAAEAQKQVKSLQSLLKDTQIQLDDAVRANDDLKENIAIVERRNNL
LQAELEELRAVVEQTERSRKLAEQELIETSERVQLLHSQNTSLINQKKKMESDLTQLQSE
VEEAVQECRNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNMEQTIKDLQHR
LDEAEQIALKGGKKQLQKLEARVRELEGELEAEQKRNAESVKGMRKSERRIKELTYQT
EEDKKNLLRLQDLVDKLQLKVKAYKRQAEEAEEQANTNLSKFRKVQHELDEAEERAD
IAESQVNKLRAKSRDIGAKQKMHDEE corresponding to amino acids 165-1939 of
MYH6_HUMAN_V3 (SEQ ID NO:340), which also corresponds to amino
acids 1-1775 of HSACMHCP_PEA.sub.--1_P28 (SEQ ID NO:333).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HSACMHCP_PEA.sub.--1_P28 (SEQ ID NO:333) also has
the following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 26, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein HSACMHCP_PEA.sub.--1_P28 (SEQ ID
NO:333) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00365 TABLE 26 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
212 P -> Q Yes 376 M -> R.sup. No 619 L -> M Yes 937 A
-> V Yes 966 A -> T No 1166 A -> .sup. No 1573 T -> S
Yes
Variant protein HSACMHCP_PEA.sub.--1_P28 (SEQ ID NO:333) is encoded
by the following transcript(s): HSACMHCP_PEA.sub.--1_T8 (SEQ ID
NO:56), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56) is shown in bold; this
coding portion starts at position 12 and ends at position 5336. The
transcript also has the following SNPs as listed in Table 27 (given
according to their position on the nucleotide sequence, with the
alternative nucleic acid listed; the last column indicates whether
the SNP is known or not; the presence of known SNPs in variant
protein HSACMHCP_PEA.sub.--1_P28 (SEQ ID NO:333) sequence provides
support for the deduced sequence of this variant protein according
to the present invention).
TABLE-US-00366 TABLE 27 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
329 G -> A Yes 646 C -> A Yes 647 A -> C Yes 674 G -> T
No 1138 T -> G No 1866 C -> A Yes 2352 C -> T Yes 2821 C
-> T Yes 2907 G -> A No 3508 C -> No 3530 G -> A Yes
3833 T -> C Yes 3836 T -> C Yes 4433 C -> T No 4499 C
-> T Yes 4721 G -> T Yes 4724 T -> C Yes 4728 A -> T
Yes 4778 C -> T Yes
Variant protein HSACMHCP_PEA.sub.--1_P29 (SEQ ID NO:334) according
to the present invention has an amino acid sequence as given at the
end of the application; it is encoded by transcript(s)
HSACMHCP_PEA.sub.--1_T14 (SEQ ID NO:58). An alignment is given to
the known protein (Myosin heavy chain, cardiac muscle alpha isoform
(SEQ ID NO:391)) at the end of the application. One or more
alignments to one or more previously published protein sequences
are given at the end of the application. A brief description of the
relationship of the variant protein according to the present
invention to each such aligned protein is as follows:
Comparison report between HSACMHCP_PEA.sub.--1_P29 (SEQ ID NO:334)
and MYH6_HUMAN_V3 (SEQ ID NO:340):
1. An isolated chimeric polypeptide encoding for
HSACMHCP_PEA.sub.--1_P29 (SEQ ID NO:334), comprising a first amino
acid sequence being at least 90% homologous to
MNKKKREAEFQKMRRDLEEATLQHEATAAALRKKHADSVAELGEQIDNLQRVKQKLEK
EKSEFKLELDDVTSNMEQIIKAKANLEKVSRTLEDQANEYRVKLEEAQRSLNDFTTQRA
KLQTENGELARQLEEKEALISQLTRGKLSYTQQMEDLKRQLEEEGKAKNALAHALQSA
RHDCDLLREQYEEETEAKAELQRVLSKANSEVAQWRTKYETDAIQRTEELEEAKKKLA
QRLQDAEEAVEAVNAKCSSLEKTKHRLQNEIEDLMVDVERSNAAAAALDKKQRNFDK
ILAEWKQKYEESQSELESSQKEARSLSTELFKLKNAYEESLEHLETFKRENKNLQEEISD
LTEQLGEGGKNVHELEKVRKQLEVEKLELQSALEEAEASLEHEEGKILRAQLEFNQIKA
EIERKLAEKDEEMEQAKRNHQRVVDSLQTSLDAETRSRNEVLRVKKKMEGDLNEMEI
QLSHANRMAAEAQKQVKSLQSLLKDTQIQLDDAVRANDDLKENIAIVERRNNLLQAEL
EELRAVVEQTERSRKLAEQELIETSERVQLLHSQNTSLINQKKKMESDLTQLQSEVEEA
VQECRNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNMEQTIKDLQHRLDEA
EQIALKGGKKQLQKLEARVRELEGELEAEQKRNAESVKGMRKSERRIKELTYQTEEDK
KNLLRLQDLVDKLQLKVKAYKRQAEEAEEQANTNLSKFRKVQHELDEAEERADIAES
QVNKLRAKSRDIGAKQKMHDEE corresponding to amino acids 1165-1939 of
MYH6_HUMAN_V3 (SEQ ID NO:340), which also corresponds to amino
acids 1-775 of HSACMHCP_PEA.sub.--1_P29 (SEQ ID NO:334).
The location of the variant protein was determined according to
results from a number of different software programs and analyses,
including analyses from SignalP and other specialized programs. The
variant protein is believed to be located as follows with regard to
the cell: intracellularly. The protein localization is believed to
be intracellularly because neither of the trans-membrane region
prediction programs predicted a trans-membrane region for this
protein. In addition both signal-peptide prediction programs
predict that this protein is a non-secreted protein.
Variant protein HSACMHCP_PEA.sub.--1_P29 (SEQ ID NO:334) also has
the following non-silent SNPs (Single Nucleotide Polymorphisms) as
listed in Table 29, (given according to their position(s) on the
amino acid sequence, with the alternative amino acid(s) listed; the
last column indicates whether the SNP is known or not; the presence
of known SNPs in variant protein HSACMHCP_PEA.sub.--1_P29 (SEQ ID
NO:334) sequence provides support for the deduced sequence of this
variant protein according to the present invention).
TABLE-US-00367 TABLE 29 Amino acid mutations SNP position(s) on
Alternative Previously amino acid sequence amino acid(s) known SNP?
166 A -> No 573 T -> S Yes
Variant protein HSACMHCP_PEA.sub.--1_P29 (SEQ ID NO:334) is encoded
by the following transcript(s): HSACMHCP_PEA.sub.--1_T14 (SEQ ID
NO:58), for which the sequence(s) is/are given at the end of the
application. The coding portion of transcript
HSACMHCP_PEA.sub.--1_T14 (SEQ ID NO:58) is shown in bold; this
coding portion starts at position 150 and ends at position 2474.
The transcript also has the following SNPs as listed in Table 30
(given according to their position on the nucleotide sequence, with
the alternative nucleic acid listed; the last column indicates
whether the SNP is known or not; the presence of known SNPs in
variant protein HSACMHCP_PEA.sub.--1_P29 (SEQ ID NO:334) sequence
provides support for the deduced sequence of this variant protein
according to the present invention).
TABLE-US-00368 TABLE 30 Nucleic acid SNPs SNP position on
Alternative Previously nucleotide sequence nucleic acid known SNP?
34 G -> T Yes 51 -> G No 646 C -> No 668 G -> A Yes 971
T -> C Yes 974 T -> C Yes 1571 C -> T No 1637 C -> T
Yes 1859 G -> T Yes 1862 T -> C Yes 1866 A -> T Yes 1916 C
-> T Yes
As noted above, cluster HSACMHCP features 65 segment(s), which were
listed in Table 2 above and for which the sequence(s) are given at
the end of the application. These segment(s) are portions of
nucleic acid sequence(s) which are described herein separately
because they are of particular interest. A description of each
segment according to the present invention is now provided.
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--2 (SEQ ID NO:209)
according to the present invention is supported by 10 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T14 (SEQ ID NO:58). Table 31 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00369 TABLE 31 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T14 (SEQ 1 328 ID NO: 58)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--20 (SEQ ID NO:210)
according to the present invention is supported by 6 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 32 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00370 TABLE 32 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 65 278 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
65 278 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 65 278 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 65 278 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
65 278 NO: 55) HSACMHCP_PEA_1_T17 (SEQ 65 278 ID NO: 59)
HSACMHCP_PEA_1_T26 (SEQ 65 278 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--22 (SEQ ID NO:211)
according to the present invention is supported by 7 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 33 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00371 TABLE 33 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 279 400 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
279 400 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 279 400 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 279 400 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
279 400 NO: 55) HSACMHCP_PEA_1_T17 (SEQ 279 400 ID NO: 59)
HSACMHCP_PEA_1_T26 (SEQ 279 400 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--25 (SEQ ID NO:212)
according to the present invention is supported by 6 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 34 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00372 TABLE 34 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 423 579 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
423 579 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 423 579 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 423 579 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
423 579 NO: 55) HSACMHCP_PEA_1_T17 (SEQ 423 579 ID NO: 59)
HSACMHCP_PEA_1_T26 (SEQ 423 579 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--43 (SEQ ID NO:213)
according to the present invention is supported by 8 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 35 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00373 TABLE 35 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 1219 1487 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 1219 1487 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 1219 1487 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 1219 1487 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 1219 1487 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 661 929 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 1219 1487 ID NO: 59) HSACMHCP_PEA_1_T26
(SEQ 1219 1487 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--45 (SEQ ID NO:214)
according to the present invention is supported by 8 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56) and
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59). Table 36 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00374 TABLE 36 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 1488 1658 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 1488 1658 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 1488 1658 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 1488 1658 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 1488 1658 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 930 1100 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 1488 1658 ID NO: 59)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--46 (SEQ ID NO:215)
according to the present invention is supported by 4 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59). Table 37 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00375 TABLE 37 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T17 (SEQ 1659 2477 ID NO: 59)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--48. (SEQ ID NO:216)
according to the present invention is supported by 1 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57). Table 38 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00376 TABLE 38 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T13 (SEQ 1 132 ID NO: 57)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--49 (SEQ ID NO:217)
according to the present invention is supported by 9 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 39 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00377 TABLE 39 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 1659 1968 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 1659 1968 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 1659 1968 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 1659 1968 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 1659 1968 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 1101 1410 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 133 442 ID NO: 57) HSACMHCP_PEA_1_T26 (SEQ
1488 1797 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--57 (SEQ ID NO:218)
according to the present invention is supported by 4 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 40 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00378 TABLE 40 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 2246 2369 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 2246 2369 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 2246 2369 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 2246 2369 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 2246 2369 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 1688 1811 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 720 843 ID NO: 57) HSACMHCP_PEA_1_T26 (SEQ
2075 2198 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--59 (SEQ ID NO:219)
according to the present invention is supported by 4 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 41 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00379 TABLE 41 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 2370 2506 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 2370 2506 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 2370 2506 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 2370 2506 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 2370 2506 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 1812 1948 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 844 980 ID NO: 57) HSACMHCP_PEA_1_T26 (SEQ
2199 2335 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--61 (SEQ ID NO:220)
according to the present invention is supported by 5 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 42 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00380 TABLE 42 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 2507 2762 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 2507 2762 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 2507 2762 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 2507 2762 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 2507 2762 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 1949 2204 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 981 1236 ID NO: 57) HSACMHCP_PEA_1_T26 (SEQ
2336 2591 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--63 (SEQ ID NO:221)
according to the present invention is supported by 6 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 43 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00381 TABLE 43 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 2763 3005 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 2763 3005 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 2763 3005 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 2763 3005 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 2763 3005 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 2205 2447 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 1237 1479 ID NO: 57) HSACMHCP_PEA_1_T26
(SEQ 2592 2834 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--65 (SEQ ID NO:222)
according to the present invention is supported by 7 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 44 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00382 TABLE 44 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3006 3182 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3006 3182 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3006 3182 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3006 3182 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3006 3182 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 2448 2624 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 1480 1656 ID NO: 57) HSACMHCP_PEA_1_T26
(SEQ 2835 3011 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--67 (SEQ ID NO:223)
according to the present invention is supported by 8 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 45 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00383 TABLE 45 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3183 3328 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3183 3328 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3183 3328 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3183 3328 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3183 3328 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 2625 2770 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 1657 1802 ID NO: 57) HSACMHCP_PEA_1_T26
(SEQ 3012 3157 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--71 (SEQ ID NO:224)
according to the present invention is supported by 10 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 46 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00384 TABLE 46 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3420 3689 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3420 3689 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3420 3689 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3420 3689 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3420 3689 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 2862 3131 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 1894 2163 ID NO: 57) HSACMHCP_PEA_1_T26
(SEQ 3249 3518 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--81 (SEQ ID NO:225)
according to the present invention is supported by 3 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52). Table 47 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00385 TABLE 47 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T3 (SEQ ID 4056 4392 NO: 52)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--87 (SEQ ID NO:226)
according to the present invention is supported by 12 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
48 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00386 TABLE 48 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4253 4436 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 4590 4773 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4253 4436 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4253 4436 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4253 4436 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3695 3878 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2727 2910 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 833 1016 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4082 4265 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--89 (SEQ ID NO:227)
according to the present invention is supported by 15 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
49 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00387 TABLE 49 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4437 4602 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 4774 4939 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4437 4602 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4437 4602 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4437 4602 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3879 4044 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2911 3076 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1017 1182 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4266 4431 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--96 (SEQ ID NO:228)
according to the present invention is supported by 16 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
50 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00388 TABLE 50 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4743 4877 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5080 5214 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4847 4981 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4743 4877 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4743 4877 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4185 4319 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3217 3351 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1323 1457 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4572 4706 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--97 (SEQ ID NO:229)
according to the present invention is supported by 16 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
51 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00389 TABLE 51 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4878 5006 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5215 5343 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4982 5110 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4878 5006 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4878 5006 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4320 4448 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3352 3480 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1458 1586 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4707 4835 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--100 (SEQ ID NO:230)
according to the present invention is supported by 19 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
52 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00390 TABLE 52 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 5037 5240 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5374 5577 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 5141 5344 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 5037 5240 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 5037 5240 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4479 4682 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3511 3714 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1617 1820 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4866 5069 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--105 (SEQ ID NO:231)
according to the present invention is supported by 1 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55). Table 53 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00391 TABLE 53 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T7 (SEQ ID 5367 5564 NO: 55)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--106 (SEQ ID NO:232)
according to the present invention is supported by 18 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
54 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00392 TABLE 54 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 5367 5642 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5704 5979 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 5471 5746 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 5367 5642 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 5565 5840 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4809 5084 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3841 4116 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1947 2222 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 5196 5471 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--107 (SEQ ID NO:233)
according to the present invention is supported by 5 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T6
(SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 55 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00393 TABLE 55 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 5643 5866 NO: 51) HSACMHCP_PEA_1_T6 (SEQ
ID 5643 5866 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID 5841 6064 NO: 55)
HSACMHCP_PEA_1_T26 (SEQ 5472 5695 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--108 (SEQ ID NO:234)
according to the present invention is supported by 7 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
56 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00394 TABLE 56 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 5867 6763 NO: 51) HSACMHCP_PEA_1_T7 (SEQ
ID 6065 6961 NO: 55) HSACMHCP_PEA_1_T26 (SEQ 5696 6592 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--111 (SEQ ID NO:235)
according to the present invention is supported by 20 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
57 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00395 TABLE 57 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 6860 6994 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 6076 6210 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 5843 5977 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 5963 6097 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 7058 7192 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 5181 5315 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 4213 4347 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 2319 2453 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 6689 6823 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--113 (SEQ ID NO:236)
according to the present invention is supported by 20 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
58 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00396 TABLE 58 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 6995 8921 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 6211 6290 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 5978 6057 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 6098 6177 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 7193 9119 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 5316 5395 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 4348 4427 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 2454 2533 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 6824 6903 ID NO:
60)
According to an optional embodiment of the present invention, short
segments related to the above cluster are also provided. These
segments are up to about 120 bp in length, and so are included in a
separate description.
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--0 (SEQ ID NO:237)
according to the present invention can be found in the following
transcript(s): HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56). Table 59
below describes the starting and ending position of this segment on
each transcript.
TABLE-US-00397 TABLE 59 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T8 (SEQ ID 1 21 NO: 56)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--3 (SEQ ID NO:238)
according to the present invention is supported by 10 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T14 (SEQ ID NO:58). Table 60 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00398 TABLE 60 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T14 (SEQ 329 374 ID NO: 58)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--4 (SEQ ID NO:239)
according to the present invention can be found in the following
transcript(s): HSACMHCP_PEA.sub.--1_T14 (SEQ ID NO:58). Table 61
below describes the starting and ending position of this segment on
each transcript.
TABLE-US-00399 TABLE 61 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T14 (SEQ 375 389 ID NO: 58)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--16 (SEQ ID NO:240)
according to the present invention is supported by 1 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 62 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00400 TABLE 62 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 1 31 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID 1
31 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 1 31 NO: 53) HSACMHCP_PEA_1_T6
(SEQ ID 1 31 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID 1 31 NO: 55)
HSACMHCP_PEA_1_T17 (SEQ 1 31 ID NO: 59) HSACMHCP_PEA_1_T26 (SEQ 1
31 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--18 (SEQ ID NO:241)
according to the present invention is supported by 3 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 63 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00401 TABLE 63 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 32 64 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
32 64 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 32 64 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 32 64 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
32 64 NO: 55) HSACMHCP_PEA_1_T17 (SEQ 32 64 ID NO: 59)
HSACMHCP_PEA_1_T26 (SEQ 32 64 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--23 (SEQ ID NO:242)
according to the present invention can be found in the following
transcript(s): HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51),
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4
(SEQ ID NO:53), HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54),
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T17
(SEQ ID NO:59) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
64 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00402 TABLE 64 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 401 422 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
401 422 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 401 422 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 401 422 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
401 422 NO: 55) HSACMHCP_PEA_1_T17 (SEQ 401 422 ID NO: 59)
HSACMHCP_PEA_1_T26 (SEQ 401 422 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--27 (SEQ ID NO:243)
according to the present invention is supported by 5 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 65 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00403 TABLE 65 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 580 607 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
580 607 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 580 607 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 580 607 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
580 607 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 22 49 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 580 607 ID NO: 59) HSACMHCP_PEA_1_T26 (SEQ
580 607 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--29 (SEQ ID NO:244)
according to the present invention is supported by 6 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 66 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00404 TABLE 66 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 608 719 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
608 719 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 608 719 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 608 719 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
608 719 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 50 161 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 608 719 ID NO: 59) HSACMHCP_PEA_1_T26 (SEQ
608 719 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--31 (SEQ ID NO:245)
according to the present invention is supported by 7 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 67 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00405 TABLE 67 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 720 812 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
720 812 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 720 812 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 720 812 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
720 812 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 162 254 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 720 812 ID NO: 59) HSACMHCP_PEA_1_T26 (SEQ
720 812 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--33 (SEQ ID NO:246)
according to the present invention is supported by 7 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 68 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00406 TABLE 68 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 813 876 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
813 876 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 813 876 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 813 876 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
813 876 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 255 318 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 813 876 ID NO: 59) HSACMHCP_PEA_1_T26 (SEQ
813 876 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--35 (SEQ ID NO:247)
according to the present invention is supported by 6 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1.sub.--T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 69 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00407 TABLE 69 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 877 975 NO: 51) HSACMHCP_PEA_1_T3 (SEQ ID
877 975 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 877 975 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 877 975 NO: 54) HSACMHCP_PEA_1_T7 (SEQ ID
877 975 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 319 417 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 877 975 ID NO: 59) HSACMHCP_PEA_1_T26 (SEQ
877 975 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--37 (SEQ ID NO:248)
according to the present invention is supported by 7 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 70 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00408 TABLE 70 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 976 1079 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 976 1079 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 976 1079 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 976 1079 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 976 1079 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 418 521 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 976 1079 ID NO: 59) HSACMHCP_PEA_1_T26 (SEQ
976 1079 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--39 (SEQ ID NO:249)
according to the present invention is supported by 8 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 71 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00409 TABLE 71 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 1080 1196 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 1080 1196 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 1080 1196 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 1080 1196 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 1080 1196 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 522 638 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 1080 1196 ID NO: 59) HSACMHCP_PEA_1_T26
(SEQ 1080 1196 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--40 (SEQ ID NO:250)
according to the present invention can be found in the following
transcript(s): HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51),
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4
(SEQ ID NO:53), HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54),
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8
(SEQ ID NO:56), HSACMHCP_PEA.sub.--1_T17 (SEQ ID NO:59) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 72 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00410 TABLE 72 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 1197 1218 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 1197 1218 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 1197 1218 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 1197 1218 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 1197 1218 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 639 660 NO: 56)
HSACMHCP_PEA_1_T17 (SEQ 1197 1218 ID NO: 59) HSACMHCP_PEA_1_T26
(SEQ 1197 1218 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--51 (SEQ ID NO:251)
according to the present invention is supported by 6 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 73 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00411 TABLE 73 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 1969 2039 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 1969 2039 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 1969 2039 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 1969 2039 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 1969 2039 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 1411 1481 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 443 513 ID NO: 57) HSACMHCP_PEA_1_T26 (SEQ
1798 1868 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--53 (SEQ ID NO:252)
according to the present invention is supported by 3 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 74 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00412 TABLE 74 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 2040 2127 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 2040 2127 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 2040 2127 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 2040 2127 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 2040 2127 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 1482 1569 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 514 601 ID NO: 57) HSACMHCP_PEA_1_T26 (SEQ
1869 1956 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--55 (SEQ ID NO:253)
according to the present invention is supported by 2 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 75 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00413 TABLE 75 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 2128 2245 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 2128 2245 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 2128 2245 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 2128 2245 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 2128 2245 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 1570 1687 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 602 719 ID NO: 57) HSACMHCP_PEA_1_T26 (SEQ
1957 2074 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--69 (SEQ ID NO:254)
according to the present invention is supported by 8 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 76 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00414 TABLE 76 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3329 3419 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3329 3419 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3329 3419 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3329 3419 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3329 3419 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 2771 2861 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 1803 1893 ID NO: 57) HSACMHCP_PEA_1_T26
(SEQ 3158 3248 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--72 (SEQ ID NO:255)
according to the present invention can be found in the following
transcript(s): HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51),
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4
(SEQ ID NO:53), HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54),
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8
(SEQ ID NO:56), HSACMHCP_PEA.sub.--1_T13 SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 77 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00415 TABLE 77 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3690 3701 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3690 3701 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3690 3701 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3690 3701 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3690 3701 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3132 3143 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2164 2175 ID NO: 57) HSACMHCP_PEA_1_T26
(SEQ 3519 3530 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--73 (SEQ ID NO:256)
according to the present invention is supported by 10 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 78 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00416 TABLE 78 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3702 3731 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3702 3731 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3702 3731 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3702 3731 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3702 3731 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3144 3173 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2176 2205 ID NO: 57) HSACMHCP_PEA_1_T26
(SEQ 3531 3560 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--74 (SEQ ID NO:257)
according to the present invention is supported by 8 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 79 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00417 TABLE 79 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3732 3809 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3732 3809 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3732 3809 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3732 3809 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3732 3809 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3174 3251 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2206 2283 ID NO: 57) HSACMHCP_PEA_1_T26
(SEQ 3561 3638 ID NO: 60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--77 (SEQ ID NO:258)
according to the present invention is supported by 12 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
80 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00418 TABLE 80 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3810 3911 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3810 3911 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3810 3911 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3810 3911 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3810 3911 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3252 3353 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2284 2385 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 390 491 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 3639 3740 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--78 (SEQ ID NO:259)
according to the present invention can be found in the following
transcript(s): HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51),
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4
(SEQ ID NO:53), HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54),
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8
(SEQ ID NO:56), HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57),
HSACMHCP_PEA.sub.--1_T14 (SEQ ID NO:58) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 81 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00419 TABLE 81 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3912 3936 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3912 3936 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3912 3936 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3912 3936 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3912 3936 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3354 3378 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2386 2410 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 492 516 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 3741 3765 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--80 (SEQ ID NO:260)
according to the present invention is supported by 14 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
82 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00420 TABLE 82 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 3937 4055 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 3937 4055 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 3937 4055 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 3937 4055 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 3937 4055 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3379 3497 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2411 2529 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 517 635 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 3766 3884 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--82 (SEQ ID NO:261)
according to the present invention can be found in the following
transcript(s): HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51),
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4
(SEQ ID NO:53), HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54),
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8
(SEQ ID NO:56), HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57),
HSACMHCP_PEA.sub.--1_T14 (SEQ ID NO:58) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 83 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00421 TABLE 83 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4056 4079 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 4393 4416 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4056 4079 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4056 4079 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4056 4079 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3498 3521 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2530 2553 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 636 659 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 3885 3908 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--83 (SEQ ID NO:262)
according to the present invention is supported by 12 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
84 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00422 TABLE 84 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4080 4145 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 4417 4482 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4080 4145 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4080 4145 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4080 4145 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3522 3587 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2554 2619 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 660 725 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 3909 3974 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--84 (SEQ ID NO:263)
according to the present invention is supported by 9 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
85 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00423 TABLE 85 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4146 4217 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 4483 4554 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4146 4217 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4146 4217 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4146 4217 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3588 3659 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2620 2691 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 726 797 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 3975 4046 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--85 (SEQ ID NO:264)
according to the present invention is supported by 10 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
86 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00424 TABLE 86 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4218 4252 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 4555 4589 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4218 4252 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4218 4252 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4218 4252 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 3660 3694 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 2692 2726 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 798 832 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4047 4081 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--90 (SEQ ID NO:265)
according to the present invention is supported by 2 libraries. The
number of libraries was determined as previously described. This
segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53). Table 87 below describes
the starting and ending position of this segment on each
transcript.
TABLE-US-00425 TABLE 87 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T4 (SEQ ID 4603 4706 NO: 53)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--91 (SEQ ID NO:266)
according to the present invention is supported by 12 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
88 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00426 TABLE 88 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4603 4679 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 4940 5016 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4707 4783 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4603 4679 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4603 4679 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4045 4121 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3077 3153 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1183 1259 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4432 4508 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--92 (SEQ ID NO:267)
according to the present invention can be found in the following
transcript(s): HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51),
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4
(SEQ ID NO:53), HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54),
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8
(SEQ ID NO:56), HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57),
HSACMHCP_PEA.sub.--1_T14 (SEQ ID NO:58) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 89 below desribes
the starting and ending position of this segment on each
transcript.
TABLE-US-00427 TABLE 89 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4680 4700 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5017 5037 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4784 4804 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4680 4700 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4680 4700 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4122 4142 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3154 3174 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1260 1280 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4509 4529 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--93 (SEQ ID NO:268)
according to the present invention is supported by 14 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
90 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00428 TABLE 90 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4701 4727 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5038 5064 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4805 4831 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4701 4727 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4701 4727 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4143 4169 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3175 3201 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1281 1307 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4530 4556 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--95 (SEQ ID NO:269)
according to the present invention can be found in the following
transcript(s): HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51),
HSACMHCP_PEA.sub.--1_T3 (SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4
(SEQ ID NO:53), HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54),
HSACMHCP_PEA.sub.--1_T7 (SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8
(SEQ ID NO:56), HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57),
HSACMHCP_PEA.sub.--1_T14 (SEQ ID NO:58) and
HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table 91 below desribes
the starting and ending position of this segment on each
transcript.
TABLE-US-00429 TABLE 91 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 4728 4742 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5065 5079 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 4832 4846 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 4728 4742 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 4728 4742 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4170 4184 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3202 3216 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1308 1322 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4557 4571 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--98 (SEQ ID NO:270)
according to the present invention is supported by 15 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
92 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00430 TABLE 92 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 5007 5036 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5344 5373 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 5111 5140 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 5007 5036 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 5007 5036 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4449 4478 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3481 3510 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1587 1616 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 4836 4865 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--103 (SEQ ID NO:271)
according to the present invention is supported by 18 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
93 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00431 TABLE 93 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 5241 5297 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5578 5634 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 5345 5401 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 5241 5297 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 5241 5297 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4683 4739 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3715 3771 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1821 1877 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 5070 5126 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--104 (SEQ ID NO:272)
according to the present invention is supported by 18 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
94 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00432 TABLE 94 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 5298 5366 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5635 5703 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 5402 5470 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 5298 5366 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 5298 5366 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 4740 4808 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 3772 3840 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 1878 1946 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 5127 5195 ID NO:
60)
Segment cluster HSACMHCP_PEA.sub.--1_node.sub.--109 (SEQ ID NO:273)
according to the present invention is supported by 18 libraries.
The number of libraries was determined as previously described.
This segment can be found in the following transcript(s):
HSACMHCP_PEA.sub.--1_T2 (SEQ ID NO:51), HSACMHCP_PEA.sub.--1_T3
(SEQ ID NO:52), HSACMHCP_PEA.sub.--1_T4 (SEQ ID NO:53),
HSACMHCP_PEA.sub.--1_T6 (SEQ ID NO:54), HSACMHCP_PEA.sub.--1_T7
(SEQ ID NO:55), HSACMHCP_PEA.sub.--1_T8 (SEQ ID NO:56),
HSACMHCP_PEA.sub.--1_T13 (SEQ ID NO:57), HSACMHCP_PEA.sub.--1_T14
(SEQ ID NO:58) and HSACMHCP_PEA.sub.--1_T26 (SEQ ID NO:60). Table
95 below describes the starting and ending position of this segment
on each transcript.
TABLE-US-00433 TABLE 95 Segment location on transcripts Segment
Segment Transcript name starting position ending position
HSACMHCP_PEA_1_T2 (SEQ ID 6764 6859 NO: 51) HSACMHCP_PEA_1_T3 (SEQ
ID 5980 6075 NO: 52) HSACMHCP_PEA_1_T4 (SEQ ID 5747 5842 NO: 53)
HSACMHCP_PEA_1_T6 (SEQ ID 5867 5962 NO: 54) HSACMHCP_PEA_1_T7 (SEQ
ID 6962 7057 NO: 55) HSACMHCP_PEA_1_T8 (SEQ ID 5085 5180 NO: 56)
HSACMHCP_PEA_1_T13 (SEQ 4117 4212 ID NO: 57) HSACMHCP_PEA_1_T14
(SEQ 2223 2318 ID NO: 58) HSACMHCP_PEA_1_T26 (SEQ 6593 6688 ID NO:
60)
Variant protein alignment to the previously known protein: Sequence
name: MYH6_HUMAN_V1 (SEQ ID NO:338) Sequence documentation:
Alignment of: HSACMHCP_PEA.sub.--1_P2 (SEQ ID
NO:326).times.MYH6.sub.--HUMAN_V1 (SEQ ID NO:338)
TABLE-US-00434 Alignment segment 1/1: Quality: 17978.00 Escore: 0
Matching length: 1855 Total length: 1855 Matching Percent 100.00
Matching Percent 100.00 Similarity: Identity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00061## ##STR00062## ##STR00063## Sequence name: MYH6_HUMAN_V2
(SEQ ID NO:339) Sequence documentation: Alignment of:
HSACMHCP_PEA.sub.--1_P3 (SEQ ID NO:327).times.MYH6.sub.--HUMAN_V2
(SEQ ID NO:339)
TABLE-US-00435 Alignment segment 1/1: Quality: 12901.00 Escore: 0
Matching length: 1328 Total length: 1328 Matching Percent 99.92
Matching Percent 99.85 Similarity: Identity: Total Percent
Similarity: 99.92 Total Percent Identity: 99.85 Gaps: 0
Alignment:
##STR00064## ##STR00065## Sequence name: MYH6_HUMAN_V2 (SEQ ID
NO:339) Sequence documentation: Alignment of:
HSACMHCP_PEA.sub.--1_P4 (SEQ ID NO:328).times.MYH6.sub.--HUMAN_V2
(SEQ ID NO:339)
TABLE-US-00436 Alignment segment 1/1: Quality: 14661.00 Escore: 0
Matching length: 1508 Total length: 1508 Matching Percent 100.00
Matching Percent 100.00 Similarity: Identity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00066## ##STR00067## ##STR00068## Sequence name: MYH6_HUMAN_V1
(SEQ ID NO:338) Sequence documentation: Alignment of:
HSACMHCP_PEA.sub.--1_P6 (SEQ ID NO:329).times.MYH6.sub.--HUMAN_V1
(SEQ ID NO:338)
TABLE-US-00437 Alignment segment 1/1: Quality: 17088.00 Escore: 0
Matching length: 1763 Total length: 1763 Matching Percent 100.00
Matching Percent 100.00 Similarity: Identity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00069## ##STR00070## ##STR00071## Sequence name: MYH6_HUMAN_V3
(SEQ ID NO:340) Sequence documentation: Alignment of:
HSACMHCP_PEA.sub.--1_P12 (SEQ ID NO:330).times.MYH6.sub.--HUMAN_V3
(SEQ ID NO:340)
TABLE-US-00438 Alignment segment 1/1: Quality: 13633.00 Escore: 0
Matching length: 1413 Total length: 1413 Matching Percent 100.00
Matching Percent 99.93 Similarity: Identity: Total Percent
Similarity: 100.00 Total Percent Identity: 99.93 Gaps: 0
Alignment:
##STR00072## ##STR00073## Sequence name: MYH6_HUMAN_V2 (SEQ ID
NO:339) Sequence documentation: Alignment of:
HSACMHCP_PEA.sub.--1_P16 (SEQ ID NO:331).times.MYH6.sub.--HUMAN_V2
(SEQ ID NO:339)
TABLE-US-00439 Alignment segment 1/1: Quality: 5155.00 Escore: 0
Matching length: 527 Total length: 527 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00074## Sequence name: MYH6_HUMAN_V1 (SEQ ID NO:338) Sequence
documentation: Alignment of: HSACMHCP_PEA.sub.--1_P25 (SEQ ID
NO:332).times.MYH6.sub.--HUMAN_V1 (SEQ ID NO:338)
TABLE-US-00440 Alignment segment 1/1: Quality: 17293.00 Escore: 0
Matching length: 1798 Total length: 1855 Matching Percent 100.00
Matching Percent 100.00 Similarity: Identity: Total Percent
Similarity: 96.93 Total Percent Identity: 96.93 Gaps: 1
Alignment:
##STR00075## ##STR00076## ##STR00077## Sequence name: MYH6_HUMAN_V3
(SEQ ID NO:340) Sequence documentation: Alignment of:
HSACMHCP_PEA.sub.--1_P28 (SEQ ID NO:333).times.MYH6.sub.--HUMAN_V3
(SEQ ID NO:340)
TABLE-US-00441 Alignment segment 1/1: Quality: 17163.00 Escore: 0
Matching length: 1775 Total length: 1775 Matching Percent 100.00
Matching Percent 100.00 Similarity: Identity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00078## ##STR00079## ##STR00080## Sequence name: MYH6_HUMAN_V3
(SEQ ID NO:340) Sequence documentation: Alignment of:
HSACMHCP_PEA.sub.--1_P29 (SEQ ID NO:334).times.MYH6.sub.--HUMAN_V3
(SEQ ID NO:340)
TABLE-US-00442 Alignment segment 1/1: Quality: 7441.00 Escore: 0
Matching length: 775 Total length: 775 Matching Percent 100.00
Matching Percent Identity: 100.00 Similarity: Total Percent
Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0
Alignment:
##STR00081##
It is appreciated that certain features of the invention, which
are, for clarity, described in the context of separate embodiments,
may also be provided in combination in a single embodiment.
Conversely, various features of the invention, which are, for
brevity, described in the context of a single embodiment, may also
be provided separately or in any suitable subcombination.
Although the invention has been described in conjunction with
specific embodiments thereof, it is evident that many alternatives,
modifications and variations will be apparent to those skilled in
the art. Accordingly, it is intended to embrace all such
alternatives, modifications and variations that fall within the
spirit and broad scope of the appended claims. All publications,
patents and patent applications mentioned in this specification are
herein incorporated in their entirety by reference into the
specification, to the same extent as if each individual
publication, patent or patent application was specifically and
individually indicated to be incorporated herein by reference. In
addition, citation or identification of any reference in this
application shall not be construed as an admission that such
reference is available as prior art to the present invention.
SEQUENCE LISTINGS
0 SQTB SEQUENCE LISTING The patent contains a lengthy "Sequence
Listing" section. A copy of the "Sequence Listing" is available in
electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US07345142B2)-
. An electronic copy of the "Sequence Listing" will also be
available from the USPTO upon request and payment of the fee set
forth in 37 CFR 1.19(b)(3).
* * * * *
References